From nakao at dev.open-bio.org  Sun Jun  4 22:52:01 2006
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Mon, 05 Jun 2006 02:52:01 +0000
Subject: [BioRuby-cvs] bioruby/test/unit/bio/io test_soapwsdl.rb,1.1,1.2
Message-ID: <200606050252.k552q1l2022218@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/test/unit/bio/io
In directory dev.open-bio.org:/tmp/cvs-serv22198/test/unit/bio/io

Modified Files:
	test_soapwsdl.rb 
Log Message:
* updated test_methods for recently added list_methods method in 
  lib/bio/io/soapwsdl.rb.


Index: test_soapwsdl.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/io/test_soapwsdl.rb,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** test_soapwsdl.rb	18 Dec 2005 17:09:53 -0000	1.1
--- test_soapwsdl.rb	5 Jun 2006 02:51:59 -0000	1.2
***************
*** 2,20 ****
  # test/unit/bio/io/test_soapwsdl.rb - Unit test for SOAP/WSDL
  #
! #   Copyright (C) 2005 Mitsuteru Nakao <n at bioruby.org>
! #
! #  This library is free software; you can redistribute it and/or
! #  modify it under the terms of the GNU Lesser General Public
! #  License as published by the Free Software Foundation; either
! #  version 2 of the License, or (at your option) any later version.
! #
! #  This library is distributed in the hope that it will be useful,
! #  but WITHOUT ANY WARRANTY; without even the implied warranty of
! #  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
! #  Lesser General Public License for more details.
! #
! #  You should have received a copy of the GNU Lesser General Public
! #  License along with this library; if not, write to the Free Software
! #  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
  #
  #  $Id$ 
--- 2,7 ----
  # test/unit/bio/io/test_soapwsdl.rb - Unit test for SOAP/WSDL
  #
! # Copytight::   Copyright (C) 2005 Mitsuteru Nakao <n at bioruby.org>
! # License::     Ruby's
  #
  #  $Id$ 
***************
*** 38,42 ****
  
    def test_methods
!     methods = ['wsdl', 'wsdl=', 'log', 'log=']
      assert_equal(methods.sort, (@obj.instance_methods - Object.methods).sort)
    end
--- 25,29 ----
  
    def test_methods
!     methods = ['list_methods','wsdl', 'wsdl=', 'log', 'log=']
      assert_equal(methods.sort, (@obj.instance_methods - Object.methods).sort)
    end


From nakao at dev.open-bio.org  Sun Jun  4 22:54:44 2006
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Mon, 05 Jun 2006 02:54:44 +0000
Subject: [BioRuby-cvs] bioruby/test/unit/bio/appl test_pts1.rb,1.1,1.2
Message-ID: <200606050254.k552sikS022267@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/test/unit/bio/appl
In directory dev.open-bio.org:/tmp/cvs-serv22247/test/unit/bio/appl

Modified Files:
	test_pts1.rb 
Log Message:
* added test_entry_id in TestPTS1Report class.


Index: test_pts1.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/appl/test_pts1.rb,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** test_pts1.rb	2 May 2006 10:29:19 -0000	1.1
--- test_pts1.rb	5 Jun 2006 02:54:42 -0000	1.2
***************
*** 106,109 ****
--- 106,113 ----
      end
  
+     def test_entry_id
+       assert_equal("hoge", @report.entry_id)
+     end
+ 
      def test_prediction
        assert_equal("Targeted", @report.prediction)


From nakao at dev.open-bio.org  Sun Jun  4 22:55:53 2006
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Mon, 05 Jun 2006 02:55:53 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl pts1.rb,1.2,1.3
Message-ID: <200606050255.k552trVs022316@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl
In directory dev.open-bio.org:/tmp/cvs-serv22296/lib/bio/appl

Modified Files:
	pts1.rb 
Log Message:
* added Bio::PTS1::Report#entry_id.


Index: pts1.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/pts1.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** pts1.rb	9 May 2006 08:18:49 -0000	1.2
--- pts1.rb	5 Jun 2006 02:55:51 -0000	1.3
***************
*** 175,178 ****
--- 175,181 ----
    class Report
  
+     # Query sequence name.
+     attr_reader :entry_id
+ 
      # Amino acids subsequence at C-terminal region.
      attr_reader :cterm
***************
*** 229,232 ****
--- 232,237 ----
        @output.each do |line|
          case line
+         when /Name<\/td><td>(\S.+)<\/td><\/tr>/
+           @entry_id = $1
          when /C-terminus<\/td><td>(\w+)<\/td>/
            @cterm = $1


From aerts at dev.open-bio.org  Wed Jun  7 08:55:52 2006
From: aerts at dev.open-bio.org (Jan Aerts)
Date: Wed, 07 Jun 2006 12:55:52 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio map.rb,1.5,1.6
Message-ID: <200606071255.k57CtqFA003705@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv3575

Modified Files:
	map.rb 
Log Message:
* Added Bio::Locations#equal? method. (Should be moved to location.rb, if approved.)
* Methods add_mapping_to_marker and add_mapping_to_map renamed to
  add_mapping_as_map and add_mapping_as_marker, respectively, to lessen the
  confusion of what is mapped to what.
* When adding a new mapping to a map or marker, a check is done first to see
  if that mapping has been added before or not.
* New method: Bio::Map::ActsLikeMarker#positions_on(map)


Index: map.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/map.rb,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** map.rb	4 May 2006 18:41:08 -0000	1.5
--- map.rb	7 Jun 2006 12:55:50 -0000	1.6
***************
*** 6,12 ****
--- 6,28 ----
  # Licence::     Ruby's
  #
+ # $Id$
  require 'bio/location'
  
  module Bio
+ 
+   # Add a method to Bio::Locations class
+   class Locations
+     def equals?(other)
+       if ! other.kind_of?(Bio::Locations)
+         return nil
+       end
+       if self.sort == other.sort
+         return true
+       else
+         return false
+       end
+     end
+   end
+ 
    # = DESCRIPTION
    # The Bio::Module contains classes that describe mapping information and can
***************
*** 42,48 ****
    #  my_map2 = Bio::Map::SimpleMap.new('consensus', 'linkage', 'cM')
    #  
!   #  my_map1.add_mapping_to_marker(my_marker1, '17')
!   #  my_map1.add_mapping_to_marker(Bio::Map::Marker.new('marker2'), '5')
!   #  my_marker3.add_mapping_to_marker(my_map1, '9')
    #  
    #  puts "Does my_map1 contain marker3? => " + my_map1.contains_marker?(my_marker3).to_s
--- 58,64 ----
    #  my_map2 = Bio::Map::SimpleMap.new('consensus', 'linkage', 'cM')
    #  
!   #  my_map1.add_mapping_as_map(my_marker1, '17')
!   #  my_map1.add_mapping_as_map(Bio::Map::Marker.new('marker2'), '5')
!   #  my_marker3.add_mapping_as_marker(my_map1, '9')
    #  
    #  puts "Does my_map1 contain marker3? => " + my_map1.contains_marker?(my_marker3).to_s
***************
*** 50,63 ****
    #  
    #  my_map1.sort.each do |mapping|
!   #    puts mapping.map.name + "\t" + mapping.marker.name + "\t" + mapping.location.from.to_s + ".." + mapping.location.to.to_s
    #  end
    #  puts my_map1.min.marker.name
    #  my_map2.each do |mapping|
!   #    puts mapping.map.name + "\t" + mapping.marker.name + "\t" + mapping.location.from.to_s + ".." + mapping.location.to.to_s
    #  end
-   #
-   # = TODO
-   # Check if initialization of @mappings can be done in ActsLikeMap and
-   # ActsLikeMarker, instead of in the classes that include these modules.
    module Map
    # = DESCRIPTION
--- 66,75 ----
    #  
    #  my_map1.sort.each do |mapping|
!   #    puts mapping.map.name + "\t" + mapping.marker.name + "\t" + mapping.location[0].from.to_s + ".." + mapping.location[-1].to.to_s
    #  end
    #  puts my_map1.min.marker.name
    #  my_map2.each do |mapping|
!   #    puts mapping.map.name + "\t" + mapping.marker.name + "\t" + mapping.location[0].from.to_s + ".." + mapping.location[-1].to.to_s
    #  end
    module Map
    # = DESCRIPTION
***************
*** 67,72 ****
--- 79,87 ----
    # * check if a given marker is mapped to it
    # , and can be mixed into other classes (e.g. Bio::Map::SimpleMap)
+   # 
+   # Classes that include this mixin should provide an array property called mappings_as_map.
      module ActsLikeMap
        include Enumerable
+       
        # = DESCRIPTION
        # Adds a Bio::Map::Mappings object to its array of mappings.
***************
*** 74,78 ****
        # = USAGE
        #   # suppose we have a Bio::Map::SimpleMap object called my_map
!       #   my_map.add_mapping_to_marker(Bio::Map::Marker.new('marker_a'), '5')
        # ---
        # *Arguments*:
--- 89,93 ----
        # = USAGE
        #   # suppose we have a Bio::Map::SimpleMap object called my_map
!       #   my_map.add_mapping_as_map(Bio::Map::Marker.new('marker_a'), '5')
        # ---
        # *Arguments*:
***************
*** 80,91 ****
        # * _location_: location of mapping. Should be a _string_, not a _number_.
        # *Returns*:: itself
!       def add_mapping_to_marker(marker, location = nil)
          unless marker.class.include?(Bio::Map::ActsLikeMarker)
            raise "[Error] marker is not object that implements Bio::Map::ActsLikeMarker"
          end
!         my_mapping = Bio::Map::Mapping.new(self, marker, Bio::Location.new(location))
!         @mappings.push(my_mapping)
!         unless marker.mapped_to?(self)
!           marker.mappings.push(my_mapping)
          end
  
--- 95,117 ----
        # * _location_: location of mapping. Should be a _string_, not a _number_.
        # *Returns*:: itself
!       def add_mapping_as_map(marker, location = nil)
          unless marker.class.include?(Bio::Map::ActsLikeMarker)
            raise "[Error] marker is not object that implements Bio::Map::ActsLikeMarker"
          end
!         my_mapping = ( location.nil? ) ? Bio::Map::Mapping.new(self, marker, nil) : Bio::Map::Mapping.new(self, marker, Bio::Locations.new(location))
!         if ! marker.mapped_to?(self)
!           self.mappings_as_map.push(my_mapping)
!           marker.mappings_as_marker.push(my_mapping)
!         else
!           already_mapped = false
!           marker.positions_on(self).each do |loc|
!             if loc.equals?(Bio::Locations.new(location))
!               already_mapped = true
!             end
!           end
!           if ! already_mapped
!             self.mappings_as_map.push(my_mapping)
!             marker.mappings_as_marker.push(my_mapping)
!           end
          end
  
***************
*** 103,107 ****
          end
          contains = false
!         @mappings.each do |mapping|
            if mapping.marker == marker
              contains = true
--- 129,133 ----
          end
          contains = false
!         self.mappings_as_map.each do |mapping|
            if mapping.marker == marker
              contains = true
***************
*** 114,118 ****
        # Go through all Bio::Map::Mapping objects linked to this Bio::Map::SimpleMap.
        def each
!         @mappings.each do |mapping|
            yield mapping
          end
--- 140,144 ----
        # Go through all Bio::Map::Mapping objects linked to this Bio::Map::SimpleMap.
        def each
!         self.mappings_as_map.each do |mapping|
            yield mapping
          end
***************
*** 126,129 ****
--- 152,157 ----
      # * check if it's mapped to a given map
      # , and can be mixed into other classes (e.g. Bio::Map::Marker)
+     # 
+     # Classes that include this mixin should provide an array property called mappings_as_marker.
      module ActsLikeMarker
        include Enumerable
***************
*** 134,138 ****
        # = USAGE
        #   # suppose we have a Bio::Map::Marker object called marker_a
!       #   marker_a.add_mapping_to_map(Bio::Map::SimpleMap.new('my_map'), '5')
        # ---
        # *Arguments*:
--- 162,166 ----
        # = USAGE
        #   # suppose we have a Bio::Map::Marker object called marker_a
!       #   marker_a.add_mapping_as_marker(Bio::Map::SimpleMap.new('my_map'), '5')
        # ---
        # *Arguments*:
***************
*** 140,151 ****
        # * _location_: location of mapping. Should be a _string_, not a _number_.
        # *Returns*:: itself
!       def add_mapping_to_map(map, location = nil)
          unless map.class.include?(Bio::Map::ActsLikeMap)
            raise "[Error] map is not object that implements Bio::Map::ActsLikeMap"
          end
!         my_mapping = Bio::Map::Mapping.new(map, self, Bio::Location.new(location))
!         @mappings.push(my_mapping)
!         unless map.contains_marker?(self)
!           map.mappings.push(my_mapping)
          end
        end
--- 168,197 ----
        # * _location_: location of mapping. Should be a _string_, not a _number_.
        # *Returns*:: itself
!       def add_mapping_as_marker(map, location = nil)
          unless map.class.include?(Bio::Map::ActsLikeMap)
            raise "[Error] map is not object that implements Bio::Map::ActsLikeMap"
          end
!         my_mapping = (location.nil?) ? Bio::Map::Mappings.new(map, self, nil) : Bio::Map::Mapping.new(map, self, Bio::Locations.new(location))
!         if ! self.mapped_to?(map)
!           self.mappings_as_marker.push(my_mapping)
!           map.mappings_as_map.push(my_mapping)
!         else
!           already_mapped = false
!           self.positions_on(map).each do |loc|
!             if loc.equals?(Bio::Locations.new(location))
!               already_mapped = true
!             end
!           end
!           if ! already_mapped
!             self.mappings_as_marker.push(my_mapping)
!             map.mappings_as_map.push(my_mapping)
!           end
!         end
!       end
! 
!       # Go through all Mapping objects linked to this marker.
!       def each
!         self.mappings_as_marker.each do |mapping|
!           yield mapping
          end
        end
***************
*** 160,166 ****
            raise "[Error] map is not object that implements Bio::Map::ActsLikeMap"
          end
! 				
          mapped = false
!         @mappings.each do |mapping|
            if mapping.map == map
              mapped = true
--- 206,212 ----
            raise "[Error] map is not object that implements Bio::Map::ActsLikeMap"
          end
! 		
          mapped = false
!         self.mappings_as_marker.each do |mapping|
            if mapping.map == map
              mapped = true
***************
*** 168,180 ****
            end
          end
          return mapped
        end
!       
!       # Go through all Mapping objects linked to this marker.
!       def each
!         @mappings.each do |mapping|
!           yield mapping
          end
        end
      end #ActsLikeMarker
  	  
--- 214,241 ----
            end
          end
+ 
          return mapped
        end
! 
!       # Return all positions of this marker on a given map.
!       # ---
!       # *Arguments*:
!       # * _map_: an object that mixes in Bio::Map::ActsLikeMap
!       # *Returns*:: array of Bio::Location objects
!       def positions_on(map)
!         unless map.class.include?(Bio::Map::ActsLikeMap)
!           raise "[Error] map is not object that implements Bio::Map::ActsLikeMap"
!         end
!         
!         positions = Array.new
!         self.mappings_as_marker.each do |mapping|
!           if mapping.map == map
!             positions.push(mapping.location)
!           end
          end
+         
+         return positions
        end
+       
      end #ActsLikeMarker
  	  
***************
*** 191,195 ****
        # * _map_: a Bio::Map::SimpleMap object
        # * _marker_: a Bio::Map::Marker object
!       # * _location_: a Bio::Location object
        def initialize (map, marker, location = nil)
          @map, @marker, @location = map, marker, location
--- 252,257 ----
        # * _map_: a Bio::Map::SimpleMap object
        # * _marker_: a Bio::Map::Marker object
!       # * _location_: a Bio::Locations object
! 
        def initialize (map, marker, location = nil)
          @map, @marker, @location = map, marker, location
***************
*** 197,219 ****
        attr_accessor :map, :marker, :location
        
!       # Compares the location of this mapping to another mapping.
!       # ---
!       # *Arguments*:
!       # * other_mapping: Bio::Map::Mapping object
!       # *Returns*::
!       # * 1 if self < other location
!       # * -1 if self > other location
!       # * 0 if both location are the same
!       # * nil if the argument is not a Bio::Location object
!       def <=>(other)
!         unless other.kind_of?(Bio::Map::Mapping)
!           raise "[Error] markers are not comparable"
!         end
! 	unless @map.equal?(other.map)
! 	  raise "[Error] maps have to be the same"
! 	end
! 
!         return self.location.<=>(other.location)
!       end
      end # Mapping
      
--- 259,280 ----
        attr_accessor :map, :marker, :location
        
! #       # Compares the location of this mapping to another mapping.
! #       # ---
! #       # *Arguments*:
! #       # * other_mapping: Bio::Map::Mapping object
! #       # *Returns*::
! #       # * 1 if self < other location
! #       # * -1 if self > other location
! #       # * 0 if both location are the same
! #       # * nil if the argument is not a Bio::Location object
! #       def <=>(other)
! #         unless other.kind_of?(Bio::Map::Mapping)
! #           raise "[Error] markers are not comparable"
! #         end
! #         unless @map.equal?(other.map)
! #           raise "[Error] maps have to be the same"
! #         end
! #         return self.location<=>(other.location) # FIXME: no <=>-method in Bio::Locations
! #       end
      end # Mapping
      
***************
*** 228,232 ****
      #   my_map1.add_marker(Bio::Map::Marker.new('marker_b', '5')
      class SimpleMap
!     include ActsLikeMap
      
        # Builds a new Bio::Map::SimpleMap object
--- 289,293 ----
      #   my_map1.add_marker(Bio::Map::Marker.new('marker_b', '5')
      class SimpleMap
!       include Bio::Map::ActsLikeMap
      
        # Builds a new Bio::Map::SimpleMap object
***************
*** 237,243 ****
        # * units: unit of the map (e.g. cM, cR, ...)
        # *Returns*:: new Bio::Map::SimpleMap object
!       def initialize (name = nil, type = nil, units = nil)
!         @name, @type, @units = name, type, units
!         @mappings = Array.new
        end
        
--- 298,304 ----
        # * units: unit of the map (e.g. cM, cR, ...)
        # *Returns*:: new Bio::Map::SimpleMap object
!       def initialize (name = nil, type = nil, length = nil, units = nil)
!         @name, @type, @length, @units = name, type, length, units
!         @mappings_as_map = Array.new
        end
        
***************
*** 247,256 ****
        # Type of the map
        attr_accessor :type
! 			
        # Units of the map
        attr_accessor :units
        
!       # Array of mappings for the map
!       attr_accessor :mappings
      end # SimpleMap
      
--- 308,321 ----
        # Type of the map
        attr_accessor :type
! 	
!       # Length of the map
!       attr_accessor :length
!       		
        # Units of the map
        attr_accessor :units
        
!       # Mappings
!       attr_accessor :mappings_as_map
!       
      end # SimpleMap
      
***************
*** 264,268 ****
      #   marker_b = Bio::Map::Marker.new('marker_b')
      class Marker
!       include ActsLikeMarker
        
        # Builds a new Bio::Map::Marker object
--- 329,333 ----
      #   marker_b = Bio::Map::Marker.new('marker_b')
      class Marker
!       include Bio::Map::ActsLikeMarker
        
        # Builds a new Bio::Map::Marker object
***************
*** 273,315 ****
        def initialize(name)
          @name = name
!         @mappings = Array.new
        end
  
        # Name of the marker
        attr_accessor :name
! 			
!       # Array of mappings for the marker
!       attr_accessor :mappings
      end # Marker
    end # Map
  end # Bio
- 
- if __FILE__ == $0
-   my_marker1 = Bio::Map::Marker.new('marker1')
- #  my_marker2 = Bio::Map::Marker.new('marker2')
-   my_marker3 = Bio::Map::Marker.new('marker3')
- 
-   my_map1 = Bio::Map::SimpleMap.new('RH_map_ABC (2006)', 'RH', 'cR')
-   my_map2 = Bio::Map::SimpleMap.new('consensus', 'linkage', 'cM')
- 
-   my_map1.add_mapping_to_marker(my_marker1, '17')
-   my_map1.add_mapping_to_marker(Bio::Map::Marker.new('marker2'), '5')
-   my_marker3.add_mapping_to_map(my_map1, '9')
- 
-   my_map2.add_mapping_to_marker(my_marker1, '57')
- 
-   puts "Does my_map1 contain marker3? => " + my_map1.contains_marker?(my_marker3).to_s
-   puts "Does my_map2 contain marker3? => " + my_map2.contains_marker?(my_marker3).to_s
- 
-   my_map1.sort.each do |mapping|
-     puts mapping.map.name + "\t" + mapping.marker.name + "\t" + mapping.location.from.to_s + ".." + mapping.location.to.to_s
-   end
-   puts my_map1.min.marker.name
- 
-   my_map2.each do |mapping|
-     puts mapping.map.name + "\t" + mapping.marker.name + "\t" + mapping.location.from.to_s + ".." + mapping.location.to.to_s
-   end
- 
- #  p my_map1.between?(my_mappable2,my_mappable3)
- #  p my_map1.between?(my_mappable,my_mappable2)
- end
--- 338,351 ----
        def initialize(name)
          @name = name
!         @mappings_as_marker = Array.new
        end
  
        # Name of the marker
        attr_accessor :name
!       
!       # Mappings
!       attr_accessor :mappings_as_marker
!       
      end # Marker
    end # Map
  end # Bio


From aerts at dev.open-bio.org  Wed Jun  7 08:56:31 2006
From: aerts at dev.open-bio.org (Jan Aerts)
Date: Wed, 07 Jun 2006 12:56:31 +0000
Subject: [BioRuby-cvs] bioruby/test/unit/bio test_map.rb,1.1,1.2
Message-ID: <200606071256.k57CuVZC003751@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/test/unit/bio
In directory dev.open-bio.org:/tmp/cvs-serv3723

Modified Files:
	test_map.rb 
Log Message:
Following changes in map.rb


Index: test_map.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/test_map.rb,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** test_map.rb	4 May 2006 16:19:52 -0000	1.1
--- test_map.rb	7 Jun 2006 12:56:29 -0000	1.2
***************
*** 5,8 ****
--- 5,10 ----
  #               Jan Aerts <jan.aerts at bbsrc.ac.uk>
  # License::     Ruby's
+ #
+ # $Id$
  
  require 'pathname'
***************
*** 14,102 ****
  
  module Bio
! 	class TestMapSimple < Test::Unit::TestCase
! 		def setup
! 			@marker1 = Bio::Map::Marker.new('marker1')
! 			@marker2 = Bio::Map::Marker.new('marker2')
! 			@map1 = Bio::Map::SimpleMap.new('map1', 'some_type', 'some_unit')
! 		end
  
! 		def test_attributes
! 			assert_equal("marker1", @marker1.name)
! 			assert_equal("marker2", @marker2.name)
! 			assert_equal([], @marker1.mappings)
! 			assert_equal([], @marker2.mappings)
! 			assert_equal("map1", @map1.name)
! 			assert_equal("some_unit", @map1.units)
! 			assert_equal("some_type", @map1.type)
! 			assert_equal([], @map1.mappings)
! 		end
! 	end
  
! 	class TestMapping < Test::Unit::TestCase
! 		def setup
! 			@marker1 = Bio::Map::Marker.new('marker1')
! 			@marker2 = Bio::Map::Marker.new('marker2')
! 			@map1 = Bio::Map::SimpleMap.new('map1', 'some_type', 'some_unit')
! 		end
  
! 		def test_add_mapping_to_marker
! 			@map1.add_mapping_to_marker(@marker2, '5')
! 			assert_equal(1, @map1.mappings.length)
! 			assert_equal(1, @marker2.mappings.length)
! 			assert_equal(0, @marker1.mappings.length)
! 			assert_kind_of(Bio::Location, @map1.mappings[0].location)
! 			assert_kind_of(Bio::Location, @marker2.mappings[0].location)
! 		end
  
!     def test_add_mapping_to_map
! 			@marker1.add_mapping_to_map(@map1, '5')
! 			assert_equal(1, @map1.mappings.length)
! 			assert_equal(1, @marker1.mappings.length)
! 			assert_kind_of(Bio::Location, @map1.mappings[0].location)
! 			assert_kind_of(Bio::Location, @marker1.mappings[0].location)
      end
! 	end
  	
! 	class CloneActsLikeMap
! 		include Bio::Map::ActsLikeMap
! 	end
  	
! 	class TestActsLikeMap < Test::Unit::TestCase
! 		def test_mixin
!       clone = CloneActsLikeMap.new
! 			assert_instance_of(CloneActsLikeMap, clone)
! 			assert_respond_to(clone, 'contains_marker?')
! 			assert_respond_to(clone, 'add_mapping_to_marker')
! 		end
! 	end
! 
! 	class CloneActsLikeMarker
! 		include Bio::Map::ActsLikeMarker
! 	end
  
! 	class TestActsLikeMarker < Test::Unit::TestCase
! 		def test_mixin
! 			clone = CloneActsLikeMarker.new
! 			assert_instance_of(CloneActsLikeMarker, clone)
! 			assert_respond_to(clone, 'mapped_to?')
! 			assert_respond_to(clone, 'add_mapping_to_map')
! 		end
! 	end
  
! 	class CloneActsLikeMapAndMarker
! 		include Bio::Map::ActsLikeMap
! 		include Bio::Map::ActsLikeMarker
! 	end
  
! 	class TestActsLikeMapAndMarker < Test::Unit::TestCase
! 		def test_mixin
! 			clone = CloneActsLikeMapAndMarker.new
! 			assert_instance_of(CloneActsLikeMapAndMarker, clone)
! 			assert_respond_to(clone, 'contains_marker?')
! 			assert_respond_to(clone, 'add_mapping_to_marker')
! 			assert_respond_to(clone, 'mapped_to?')
! 			assert_respond_to(clone, 'add_mapping_to_map')
! 		end
! 	end
  
  end
--- 16,184 ----
  
  module Bio
!   class TestMapSimple < Test::Unit::TestCase
!     def setup
!       @marker1 = Bio::Map::Marker.new('marker1')
!       @marker2 = Bio::Map::Marker.new('marker2')
!       @map1 = Bio::Map::SimpleMap.new('map1', 'some_type', 500, 'some_unit')
!     end
  
!     def test_attributes
!       assert_equal("marker1", @marker1.name)
!       assert_equal("marker2", @marker2.name)
!       assert_equal([], @marker1.mappings_as_marker)
!       assert_equal([], @marker2.mappings_as_marker)
!       assert_equal("map1", @map1.name)
!       assert_equal("some_unit", @map1.units)
!       assert_equal("some_type", @map1.type)
!       assert_equal([], @map1.mappings_as_map)
!     end
!   end
  
!   class TestMapping < Test::Unit::TestCase
!     def setup
!       @marker1 = Bio::Map::Marker.new('marker1')
!       @marker2 = Bio::Map::Marker.new('marker2')
!       @marker3 = Bio::Map::Marker.new('marker3')
!       @map1 = Bio::Map::SimpleMap.new('map1', 'some_type', 'some_unit')
!     end
  
!     def test_add_mapping_as_map
!       @map1.add_mapping_as_map(@marker2, '5')
!       assert_equal(1, @map1.mappings_as_map.length)
!       assert_equal(1, @marker2.mappings_as_marker.length)
!       assert_equal(0, @marker1.mappings_as_marker.length)
!       assert_kind_of(Bio::Locations, @map1.mappings_as_map[0].location)
!       assert_kind_of(Bio::Locations, @marker2.mappings_as_marker[0].location)
!     end
  
!     def test_add_mapping_as_marker
!       @marker1.add_mapping_as_marker(@map1, '5')
!       assert_equal(1, @map1.mappings_as_map.length, 'Mapping as map')
!       assert_equal(1, @marker1.mappings_as_marker.length, 'Mapping as marker')
!       assert_kind_of(Bio::Locations, @map1.mappings_as_map[0].location)
!       assert_kind_of(Bio::Locations, @marker1.mappings_as_marker[0].location)
      end
!     
!     def test_mapped_to?
!       @marker1.add_mapping_as_marker(@map1, '5')
!       assert_equal(true, @marker1.mapped_to?(@map1))
!       assert_equal(false, @marker3.mapped_to?(@map1))
!     end
!     
!     def test_contains_marker?
!       @marker1.add_mapping_as_marker(@map1, '5')
!       assert_equal(true, @map1.contains_marker?(@marker1))
!       assert_equal(false, @map1.contains_marker?(@marker3))
!     end
!     
!     def test_mappings_as_map_each
!       @map1.add_mapping_as_map(@marker1, '5')
!       @marker2.add_mapping_as_marker(@map1, '7')
!       mappings = 0
!       @map1.mappings_as_map.each do |mapping|
!         mappings += 1
!       end
!       assert_equal(2, mappings)
!     end
! 
!     def test_mappings_as_marker_each
!       @map1.add_mapping_as_map(@marker1, '5')
!       @marker1.add_mapping_as_marker(@map1, '7')
!       mappings = 0
!       @marker1.mappings_as_marker.each do |mapping|
!         mappings += 1
!       end
!       assert_equal(2, mappings)
!       
!     end
!     
!     def test_multiple_mappings_between_same_marker_and_map
!       @map1.add_mapping_as_map(@marker1, '5')
!       @map1.add_mapping_as_map(@marker1, '37')
!       @marker1.add_mapping_as_marker(@map1, '53')
!       assert_equal(3, @marker1.mappings_as_marker.length)
! 
!       @marker1.add_mapping_as_marker(@map1, '53')  # This mapping should _not_ be added, because it's already defined.
!       assert_equal(3, @marker1.mappings_as_marker.length)
!     end
!     
!     def test_positions_on
!       @map1.add_mapping_as_map(@marker1, '5')
!       assert_equal(1, @marker1.mappings_as_marker.length)
!       assert_equal('5', @marker1.positions_on(@map1).collect{|p| p.first.from.to_s}.join(',')) # FIXME: Test is not correct (uses Location.first)
!       @map1.add_mapping_as_map(@marker1, '37')
!       assert_equal('5,37', @marker1.positions_on(@map1).collect{|p| p.first.from.to_s}.sort{|a,b| a.to_i <=> b.to_i}.join(',')) # FIXME: Test is not correct (uses Location.first)
!     end
!   end
  	
!   class CloneActsLikeMap
!     include Bio::Map::ActsLikeMap
!     def initialize
!       @mappings_as_map = Array.new
!     end
!     attr_accessor :mappings_as_map
!   end
  	
!   class TestActsLikeMap < Test::Unit::TestCase
!     def setup
!       @clone = CloneActsLikeMap.new
!     end
!     def test_mixin
!       assert_instance_of(CloneActsLikeMap, @clone)
!       assert_respond_to(@clone, 'contains_marker?')
!       assert_respond_to(@clone, 'add_mapping_as_map')
!       assert_equal(0, @clone.mappings_as_map.length)
!     end
!   end
  
!   class CloneActsLikeMarker
!     include Bio::Map::ActsLikeMarker
!     def initialize
!       @mappings_as_marker = Array.new
!     end
!     attr_accessor :mappings_as_marker
!   end
  
!   class TestActsLikeMarker < Test::Unit::TestCase
!     def setup
!       @clone = CloneActsLikeMarker.new
!     end
!     
!     def test_mixin
!       assert_instance_of(CloneActsLikeMarker, @clone)
!       assert_respond_to(@clone, 'mapped_to?')
!       assert_respond_to(@clone, 'add_mapping_as_marker')
!     end
!   end
  
!   class CloneActsLikeMapAndMarker
!     include Bio::Map::ActsLikeMap
!     include Bio::Map::ActsLikeMarker
!     def initialize
!       @mappings_as_map = Array.new
!       @mappings_as_marker = Array.new
!     end
!     attr_accessor :mappings_as_map, :mappings_as_marker
!   end
  
+   class TestActsLikeMapAndMarker < Test::Unit::TestCase
+     def setup
+       @clone_a = CloneActsLikeMapAndMarker.new
+       @clone_b = CloneActsLikeMapAndMarker.new
+       @clone_a.add_mapping_as_map(@clone_b, nil)
+     end
+     
+     def test_mixin
+       assert_instance_of(CloneActsLikeMapAndMarker, @clone_a)
+       assert_respond_to(@clone_a, 'contains_marker?')
+       assert_respond_to(@clone_a, 'add_mapping_as_map')
+       assert_respond_to(@clone_a, 'mapped_to?')
+       assert_respond_to(@clone_a, 'add_mapping_as_marker')
+       
+       assert_equal(1, @clone_a.mappings_as_map.length)
+       assert_equal(0, @clone_a.mappings_as_marker.length)
+       assert_equal(0, @clone_b.mappings_as_map.length)
+       assert_equal(1, @clone_b.mappings_as_marker.length)
+     end
+   end
  end


From ngoto at dev.open-bio.org  Mon Jun 12 06:35:44 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Mon, 12 Jun 2006 10:35:44 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/io flatfile.rb,1.49,1.50
Message-ID: <200606121035.k5CAZiau015926@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/io
In directory dev.open-bio.org:/tmp/cvs-serv15886/lib/bio/io

Modified Files:
	flatfile.rb 
Log Message:
Bio::FlatFile.open(klass, filename) didn't work.


Index: flatfile.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/flatfile.rb,v
retrieving revision 1.49
retrieving revision 1.50
diff -C2 -d -r1.49 -r1.50
*** flatfile.rb	22 Mar 2006 10:19:22 -0000	1.49
--- flatfile.rb	12 Jun 2006 10:35:42 -0000	1.50
***************
*** 426,430 ****
        unless file.respond_to?(:gets)
          # 'file' is a filename
!         self.open_file(file, *arg, &block)
        else
          # 'file' is a IO object
--- 426,430 ----
        unless file.respond_to?(:gets)
          # 'file' is a filename
!         _open_file(dbclass, file, *arg, &block)
        else
          # 'file' is a IO object
***************
*** 466,478 ****
      #
      def self.open_file(filename, *arg)
        if block_given? then
          BufferedInputStream.open_file(filename, *arg) do |stream|
!           yield self.new(nil, stream)
          end
        else
          stream = BufferedInputStream.open_file(filename, *arg)
!         self.new(nil, stream)
        end
      end
  
      # Opens URI specified as _uri_.
--- 466,490 ----
      #
      def self.open_file(filename, *arg)
+       _open_file(nil, filename, *arg)
+     end
+ 
+     # Same as FlatFile.open(dbclass, filename, *arg),
+     # except that it only accept filename and doesn't accept IO object.
+     #
+     # It can accept a block.
+     # If a block is given, it returns the block's return value.
+     # Otherwise, it returns a new FlatFile object.
+     #
+     def self._open_file(dbclass, filename, *arg)
        if block_given? then
          BufferedInputStream.open_file(filename, *arg) do |stream|
!           yield self.new(dbclass, stream)
          end
        else
          stream = BufferedInputStream.open_file(filename, *arg)
!         self.new(dbclass, stream)
        end
      end
+     private_class_method :_open_file
  
      # Opens URI specified as _uri_.


From ngoto at dev.open-bio.org  Thu Jun 15 10:28:57 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Thu, 15 Jun 2006 14:28:57 +0000
Subject: [BioRuby-cvs] bioruby/test/unit/bio/io test_flatfile.rb,NONE,1.1
Message-ID: <200606151428.k5FESvlN028352@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/test/unit/bio/io
In directory dev.open-bio.org:/tmp/cvs-serv28332/test/unit/bio/io

Added Files:
	test_flatfile.rb 
Log Message:
Unit test for Bio::FlatFile class is added but still incomplete.


--- NEW FILE: test_flatfile.rb ---
#
# = test/unit/bio/io/test_flatfile.rb - unit test for Bio::FlatFile
#
#   Copyright (C) 2006 Naohisa Goto <ng at bioruby.org>
#
# License:: Ruby's
#
#  $Id: test_flatfile.rb,v 1.1 2006/06/15 14:28:55 ngoto Exp $
#

require 'pathname'
libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
$:.unshift(libpath) unless $:.include?(libpath)

require 'test/unit'
require 'bio'
require 'stringio'


module Bio
    
module TestFlatFile

  bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4)).cleanpath.to_s
  TestDataPath = Pathname.new(File.join(bioruby_root, 'test', 'data')).cleanpath.to_s
  TestDataFastaFormat01 = File.join(TestDataPath, 'fasta', 'example1.txt')

  class TestBufferedInputStreamClassMethod < Test::Unit::TestCase
    def test_self_for_io
      io = File.open(TestDataFastaFormat01)
      obj = Bio::FlatFile::BufferedInputStream.for_io(io)
      assert_instance_of(Bio::FlatFile::BufferedInputStream, obj)
      assert_equal(TestDataFastaFormat01, obj.path)
    end

    def test_self_open_file
      obj = Bio::FlatFile::BufferedInputStream.open_file(TestDataFastaFormat01)
      assert_instance_of(Bio::FlatFile::BufferedInputStream, obj)
      assert_equal(TestDataFastaFormat01, obj.path)
    end

    def test_self_open_file_with_block
      obj2 = nil
      Bio::FlatFile::BufferedInputStream.open_file(TestDataFastaFormat01) do |obj|
        assert_instance_of(Bio::FlatFile::BufferedInputStream, obj)
        assert_equal(TestDataFastaFormat01, obj.path)
        obj2 = obj
      end
      assert_raise(IOError) { obj2.close }
    end
  end #class TestBufferedInputStreamClassMethod

  class TestBufferedInputStream < Test::Unit::TestCase
    def setup
      io = File.open(TestDataFastaFormat01)
      path = TestDataFastaFormat01
      @obj = Bio::FlatFile::BufferedInputStream.new(io, path)
    end

    def test_to_io
      assert_kind_of(IO, @obj.to_io)
    end

    def test_close
      assert_nil(@obj.close)
    end

    def test_rewind
      @obj.prefetch_gets
      @obj.rewind
      assert_equal('', @obj.prefetch_buffer)
    end

    def test_pos
      @obj.gets
      @obj.gets
      @obj.prefetch_gets
      assert_equal(117, @obj.pos) #the number depends on original data
    end

    def test_pos=()
      str = @obj.gets
      assert_equal(0, @obj.pos = 0)
    end
      
    def test_eof_false_first
      assert_equal(false, @obj.eof?)
    end

    def test_eof_false_after_prefetch
      while @obj.prefetch_gets; nil; end
      assert_equal(false, @obj.eof?)
    end

    def test_eof_true
      while @obj.gets; nil; end
      assert_equal(true, @obj.eof?)
    end

    def test_gets
      @obj.gets
      @obj.gets
      assert_equal("gagcaaatcgaaaaggagagatttctgcatatcaagagaaaattcgagctgagatacattccaagtgtggctactc", @obj.gets.chomp)
    end

    def test_gets_equal_prefetch_gets
      @obj.prefetch_gets
      str = @obj.prefetch_gets
      @obj.prefetch_gets
      @obj.gets
      assert_equal(@obj.gets, str)
    end

    def test_ungets
      @obj.gets
      @obj.gets
      str1 = @obj.gets
      str2 = @obj.gets
      assert_nil(@obj.ungets(str2))
      assert_nil(@obj.ungets(str1))
      assert_equal(str1, @obj.gets)
      assert_equal(str2, @obj.gets)
    end

    def test_getc
      assert_equal(?>, @obj.getc)
    end

    def test_getc_after_prefetch
      @obj.prefetch_gets
      assert_equal(?>, @obj.getc)
    end

    def test_ungetc
      c = @obj.getc
      assert_nil(@obj.ungetc(c))
      assert_equal(c, @obj.getc)
    end

    def test_ungetc_after_prefetch
      str = @obj.prefetch_gets
      c = @obj.getc
      assert_nil(@obj.ungetc(c))
      assert_equal(str, @obj.gets)
    end

    def test_prefetch_buffer
      str = @obj.prefetch_gets
      str += @obj.prefetch_gets
      assert_equal(str, @obj.prefetch_buffer)
    end

    def test_prefetch_gets
      @obj.prefetch_gets
      @obj.prefetch_gets
      @obj.gets
      str = @obj.prefetch_gets
      @obj.gets
      assert_equal(str, @obj.gets)
    end

    def test_prefetch_gets_with_arg
      # test @obj.gets
      str = @obj.prefetch_gets("\n>")
      assert_equal(str, @obj.gets("\n>"))
      # test using IO object
      io = @obj.to_io
      io.rewind
      assert_equal(str, io.gets("\n>"))
    end

    def test_skip_spaces
      @obj.gets('CDS')
      assert_nil(@obj.skip_spaces)
      assert_equal(?a, @obj.getc)
    end
                   
  end #class TestBufferedInputStream

  class TestFlatFileWithCustomClass < Test::Unit::TestCase

    # very simple parser for tab-separated data
    class SimpleFormat
      # delimiter needed for flatfile
      DELIMITER = RS = nil # nil means no delimiter and reading entire file
      def initialize(str)
        @data = str.split(/\n/).collect { |x| x.to_s.split(/\t/) }
      end
      attr_reader :data
    end

    def test_simpleformat
      testdata = "AAA\tBBB\tCCCCC\tDDDD\n123\t456\n"
      testio = StringIO.new(testdata)
      Bio::FlatFile.open(SimpleFormat, testio) do |ff|
        ff.each do |entry|
          assert_equal([ [ 'AAA', 'BBB', 'CCCCC', 'DDDD' ],
                         [ '123', '456' ] ], entry.data)
        end
      end
    end

    # very simple parser for "//"-separated entries
    class SimpleFormat2
      # delimiter needed for flatfile
      DELIMITER = RS = "//\n" # the end of each entry is "//\n"
      def initialize(str)
        # very simple parser only to store a text data
        @data = str
      end
      attr_reader :data
    end

    def test_simpleformat2
      testdata = <<__END_OF_TESTDATA__
test01
This is a test.
//
test02
This is an example.
//
__END_OF_TESTDATA__
      a = testdata.split(/(\/\/\n)/)
      results = [ a[0]+a[1], a[2]+a[3] ]
      testio = StringIO.new(testdata)
      Bio::FlatFile.open(SimpleFormat2, testio) do |ff|
        ff.each do |entry|
          assert_equal(results.shift, entry.data)
        end
      end
    end

  end #class TestFlatFileWithCustomClass

end #module TestFlatFile

end #module Bio


From nakao at dev.open-bio.org  Fri Jun 16 12:51:07 2006
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Fri, 16 Jun 2006 16:51:07 +0000
Subject: [BioRuby-cvs] bioruby/test/unit/bio/db/embl test_sptr.rb,1.2,1.3
Message-ID: <200606161651.k5GGp7aH001256@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/test/unit/bio/db/embl
In directory dev.open-bio.org:/tmp/cvs-serv1236

Modified Files:
	test_sptr.rb 
Log Message:
* Added a test in test_ft.


Index: test_sptr.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/db/embl/test_sptr.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** test_sptr.rb	23 Nov 2005 10:06:12 -0000	1.2
--- test_sptr.rb	16 Jun 2006 16:51:05 -0000	1.3
***************
*** 234,238 ****
        assert(@obj.ft)
        name = 'DNA_BIND'
!       assert_equal([{"FTId"=>nil, "From"=>102, "diff"=>[], "To"=>292, "Description"=>nil}], @obj.ft(name))
      end
  
--- 234,239 ----
        assert(@obj.ft)
        name = 'DNA_BIND'
!       assert_equal([{"FTId"=>"", "From"=>102, "diff"=>[], "To"=>292, "Description"=>""}], @obj.ft(name))
!       assert_equal([{"FTId"=>"", "From"=>102, "diff"=>[], "To"=>292, "Description"=>""}], @obj.ft[name])
      end
  


From nakao at dev.open-bio.org  Fri Jun 16 13:01:03 2006
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Fri, 16 Jun 2006 17:01:03 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/db/embl sptr.rb,1.31,1.32
Message-ID: <200606161701.k5GH13j4001328@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/db/embl
In directory dev.open-bio.org:/tmp/cvs-serv1306

Modified Files:
	sptr.rb 
Log Message:
* fixed a PROPEP parsing bug in Bio::SPTR#ft. (reported by Makoto 
  Hamaguchi-san).
* changed codes in the Bio::SPTR#id_line and the Bio::SPTR#dt. [refactoring] 


Index: sptr.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/embl/sptr.rb,v
retrieving revision 1.31
retrieving revision 1.32
diff -C2 -d -r1.31 -r1.32
*** sptr.rb	14 Apr 2006 05:52:28 -0000	1.31
--- sptr.rb	16 Jun 2006 17:01:01 -0000	1.32
***************
*** 2,6 ****
  # = bio/db/embl/sptr.rb - UniProt/SwissProt and TrEMBL database class
  # 
! # Copyright::   Copyright (C) 2001-2006 Mitsuteru C. Nakao <n at bioruby.org>
  # License::     Ruby's
  #
--- 2,6 ----
  # = bio/db/embl/sptr.rb - UniProt/SwissProt and TrEMBL database class
  # 
! # Copyright::   Copyright (C) 2001-2006  Mitsuteru C. Nakao <n at bioruby.org>
  # License::     Ruby's
  #
***************
*** 46,50 ****
    @@data_class = ["STANDARD", "PRELIMINARY"]
  
-   
    # returns a Hash of the ID line.
    #
--- 46,49 ----
***************
*** 57,84 ****
    #
    # === Examples
!   #   obj.id_line  #=> {"ENTRY_NAME"=>"P53_HUMAN", "DATA_CLASS"=>"STANDARD", "SEQUENCE_LENGTH"=>393, "MOLECULE_TYPE"=>"PRT"}
    #
    #   obj.id_line('ENTRY_NAME') #=> "P53_HUMAN"
    #
    def id_line(key = nil)
!     unless @data['ID']
!       tmp = Hash.new
!       a = @orig['ID'].split(/ +/)         
!       tmp['ENTRY_NAME']      = a[1]
!       tmp['DATA_CLASS']      = a[2].sub(/;/,'') 
!       tmp['MOLECULE_TYPE']   = a[3].sub(/;/,'')
!       tmp['SEQUENCE_LENGTH'] = a[4].to_i
!       @data['ID'] = tmp
!     end
  
!     if key
!       @data['ID'][key] # String/Int
!     else
!       @data['ID']      # Hash
!     end
    end
  
  
- 
    # returns a ENTRY_NAME in the ID line. 
    #
--- 56,78 ----
    #
    # === Examples
!   #   obj.id_line  #=> {"ENTRY_NAME"=>"P53_HUMAN", "DATA_CLASS"=>"STANDARD", 
!   #                     "SEQUENCE_LENGTH"=>393, "MOLECULE_TYPE"=>"PRT"}
    #
    #   obj.id_line('ENTRY_NAME') #=> "P53_HUMAN"
    #
    def id_line(key = nil)
!     return id_line[key] if key
!     return @data['ID'] if @data['ID']
  
!     part = @orig['ID'].split(/ +/)         
!     @data['ID'] = {
!       'ENTRY_NAME'      => part[1],
!       'DATA_CLASS'      => part[2].sub(/;/,''),
!       'MOLECULE_TYPE'   => part[3].sub(/;/,''),
!       'SEQUENCE_LENGTH' => part[4].to_i 
!     }
    end
  
  
    # returns a ENTRY_NAME in the ID line. 
    #
***************
*** 128,145 ****
    #   DT DD-MMM-YYY (rel. NN, Last annotation update)
    def dt(key = nil)
!     unless @data['DT']
!       tmp = Hash.new
!       a = self.get('DT').split(/\n/)
!       tmp['created']    = a[0].sub(/\w{2}   /,'').strip
!       tmp['sequence']   = a[1].sub(/\w{2}   /,'').strip
!       tmp['annotation'] = a[2].sub(/\w{2}   /,'').strip
!       @data['DT'] = tmp
!     end
  
!     if key
!       @data['DT'][key]
!     else
!       @data['DT']
!     end
    end
  
--- 122,134 ----
    #   DT DD-MMM-YYY (rel. NN, Last annotation update)
    def dt(key = nil)
!     return dt[key] if key
!     return @data['DT'] if @data['DT']
  
!     part = self.get('DT').split(/\n/)
!     @data['DT'] = {
!       'created'    => part[0].sub(/\w{2}   /,'').strip,
!       'sequence'   => part[1].sub(/\w{2}   /,'').strip,
!       'annotation' => part[2].sub(/\w{2}   /,'').strip
!     }
    end
  
***************
*** 451,455 ****
  
        # Event, Named isoforms, Comment, [Name, Synonyms, IsoId, Sequnce]+
!       tmp = {'Event' => nil, 'Named isoforms' => nil, 'Comment' => nil, 'Variants'  => []}
  
        if /Event=(.+?);/ =~ ap
--- 440,445 ----
  
        # Event, Named isoforms, Comment, [Name, Synonyms, IsoId, Sequnce]+
!       tmp = {'Event' => nil, 'Named isoforms' => nil, 'Comment' => nil, 
!              'Variants'  => []}
  
        if /Event=(.+?);/ =~ ap
***************
*** 499,503 ****
  
        ms.each do |m|
!         mass = {'MW'=>nil,'MW_ERR'=>nil,'METHOD'=>nil,'RANGE'=>nil}
          m.sub(/.$/,'').split(/;/).each do |line|
            case line
--- 489,493 ----
  
        ms.each do |m|
!         mass = {'MW' => nil,'MW_ERR' => nil,'METHOD' => nil,'RANGE' => nil}
          m.sub(/.$/,'').split(/;/).each do |line|
            case line
***************
*** 550,554 ****
      it.map {|ent|
        {:partner_id => ent[0].strip,
!        :nbexp => ent[1].strip, 
         :intact_acc => ent[2].split(', ') }
      }
--- 540,544 ----
      it.map {|ent|
        {:partner_id => ent[0].strip,
!        :nbexp      => ent[1].strip, 
         :intact_acc => ent[2].split(', ') }
      }
***************
*** 577,583 ****
  
    # returns conteins in the feature table.
    # * Bio::SPTR#ft -> Hash
!   #    {'feature_name' => [{'From' => str, 'To' => str,
!   #                         'Description' => str, 'FTId' => str}],...}
    #
    # returns an Array of the information about the feature_name in the feature table.
--- 567,589 ----
  
    # returns conteins in the feature table.
+   #
+   # == Examples
+   #
+   #  sp = Bio::SPTR.new(entry)
+   #  ft = sp.ft
+   #  ft.class #=> Hash
+   #  ft.keys.each do |feature_key|
+   #    ft[feature_key].each do |feature|
+   #      feature['From'] #=> '1'
+   #      feature['To']   #=> '21'
+   #      feature['Description'] #=> ''
+   #      feature['FTId'] #=> ''
+   #      feature['diff'] #=> []
+   #    end
+   #  end
+   #
    # * Bio::SPTR#ft -> Hash
!   #    {FEATURE_KEY => [{'From' => int, 'To' => int, 'diff' => [],
!   #                      'Description' => aStr, 'FTId' => aStr}],...}
    #
    # returns an Array of the information about the feature_name in the feature table.
***************
*** 595,692 ****
    #   35-75   Description (>=0 per key)
    #   -----   -----------------
!   def ft(feature_name = nil)
!     unless @data['FT']
!       table        = Hash.new()
!       last_feature = nil
! 
!       begin
!         get('FT').split(/\n/).each {|line|
! 
!           feature = line[5..12].strip
! 
!           if feature == '' and line[34..74]
!             tmp = ' ' + line[34..74].strip 
!             table[last_feature].last['Description'] << tmp
!             
!             next unless /\.$/ =~ line
!           else
!             from = line[14..19].strip
!             to   = line[21..26].strip
!             desc = line[34..74].strip if line[34..74]
  
!             table[feature] = [] unless table[feature]
!             table[feature] << {
!               'From'        => from.to_i, 
!               'To'          => to.to_i, 
!               'Description' => desc,
!               'diff'        => [],
!               'FTId'        => nil }
!             last_feature = feature
!             next
!           end
  
!           case last_feature
!           when 'VARSPLIC', 'VARIANT', 'CONFLICT'
!             if /FTId=(.+?)\./ =~ line   # version 41 >
!               ftid = $1
!               table[last_feature].last['FTId'] = ftid
!               table[last_feature].last['Description'].sub!(/ \/FTId=#{ftid}./,'') 
!             end
  
!             case table[last_feature].last['Description']
!             when /(\w[\w ]*\w*) - ?> (\w[\w ]*\w*)/
!               original = $1
!               swap = $2
!               original = original.gsub(/ /,'').strip
!               swap = swap.gsub(/ /,'').strip
!             when /Missing/i
!               original = seq.subseq(table[last_feature].last['From'],
!                                     table[last_feature].last['To'])
!               swap = ''
!             else
!               raise line
!             end
!             table[last_feature].last['diff'] = [original, swap]
!           end
!         }
  
!       rescue
!         raise "Invalid FT Lines(#{$!}) in #{entry_id}:, \n" + 
!                   "'#{self.get('FT')}'\n"
!       end
  
!       table.each_key do |k|
!         table[k].each do |e|
!           if / -> / =~ e['Description']
!             pattern = /([A-Z][A-Z ]*[A-Z]*) -> ([A-Z][A-Z ]*[A-Z]*)/
!             e['Description'].sub!(pattern) {  
!               a = $1
!               b = $2
!               a.gsub(/ /,'') + " -> " + b.gsub(/ /,'') 
!             }
!           end
!           if /- [\w\d]/ =~ e['Description']
!             e['Description'].gsub!(/([\w\d]- [\w\d]+)/) { 
!               a = $1
!               if /- AND/ =~ a
!                 a
!               else
!                 a.sub(/ /,'') 
!               end
!             }
!           end
          end
        end
-       @data['FT'] = table
      end
! 
!     if feature_name
!       @data['FT'][feature_name]
!     else
!       @data['FT']
      end
    end
  
  
    # returns a Hash of conteins in the SQ lines.
    # * Bio::SPTRL#sq  -> hsh
--- 601,670 ----
    #   35-75   Description (>=0 per key)
    #   -----   -----------------
!   #
!   def ft(feature_key = nil)
!     return ft[feature_key] if feature_key
!     return @data['FT'] if @data['FT']
  
!     table = []
!     begin
!     get('FT').split("\n").each do |line|
!       if line =~ /^FT   \w/
!         feature = line.chomp.ljust(74)
!         table << [feature[ 5..12].strip,   # Feature Name
!                   feature[14..19].strip,   # From
!                   feature[21..26].strip,   # To
!                   feature[34..74].strip ]  # Description
!       else
!         table.last << line.chomp.sub!(/^FT +/, '')
!       end
!     end
  
!     # Join Desctiption lines
!     table = table.map { |feature| 
!       ftid = feature.pop if feature.last =~ /FTId=/
!       if feature.size > 4
!         feature = [feature[0], feature[1], feature[2], 
!                    feature[3, feature.size - 3].join(" ")]
!       end
!       feature << ftid
!     }
  
!     hash = {}
!     table.each do |feature|
!       hash[feature[0]] = [] unless hash[feature[0]]
  
!       hash[feature[0]] << {
!         'From' => feature[1].to_i, 
!         'To'   => feature[2].to_i, 
!         'Description' => feature[3], 
!         'FTId' => feature[4].to_s.sub(/\/FTId=/, '').sub(/\.$/, ''),
!         'diff' => []
!       }
  
!       case feature[0]
!       when 'VARSPLIC', 'VARIANT', 'VAR_SEQ', 'CONFLICT'
!         case hash[feature[0]].last['Description']
!         when /(\w[\w ]*\w*) - ?> (\w[\w ]*\w*)/
!           original_res = $1
!           changed_res = $2
!           original_res = original_res.gsub(/ /,'').strip
!           chenged_res = changed_res.gsub(/ /,'').strip
!         when /Missing/i
!           original_res = seq.subseq(hash[feature[0]].last['From'],
!                                     hash[feature[0]].last['To'])
!           changed_res = ''
          end
+         hash[feature[0]].last['diff'] = [original_res, chenged_res]
        end
      end
!     rescue
!       raise "Invalid FT Lines(#{$!}) in #{entry_id}:, \n'#{self.get('FT')}'\n"
      end
+ 
+     @data['FT'] = hash
    end
  
  
+ 
    # returns a Hash of conteins in the SQ lines.
    # * Bio::SPTRL#sq  -> hsh
***************
*** 694,698 ****
    # returns a value of a key given in the SQ lines.
    # * Bio::SPTRL#sq(key)  -> int or str
!   # * Keys: ['MW', 'mw', 'molecular', 'weight', 'aalen', 'len', 'length', 'CRC64']
    #
    # === SQ Line; sequence header (1/entry)
--- 672,677 ----
    # returns a value of a key given in the SQ lines.
    # * Bio::SPTRL#sq(key)  -> int or str
!   # * Keys: ['MW', 'mw', 'molecular', 'weight', 'aalen', 'len', 'length', 
!   #          'CRC64']
    #
    # === SQ Line; sequence header (1/entry)


From ngoto at dev.open-bio.org  Tue Jun 20 10:21:37 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Tue, 20 Jun 2006 14:21:37 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/blat report.rb,1.7,1.8
Message-ID: <200606201421.k5KELbnB001117@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl/blat
In directory dev.open-bio.org:/tmp/cvs-serv1058

Modified Files:
	report.rb 
Log Message:
Added Bio::BLAT::Report::Hit#milli_bad, #percent_identity, #protein?,
and #score methods. The algorithm of these methods are described in
the BLAT FAQ (http://genome.ucsc.edu/FAQ/FAQblat#blat5).
Thanks to Dr. Itoshi Nikaido for help.


Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blat/report.rb,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** report.rb	8 May 2006 14:37:55 -0000	1.7
--- report.rb	20 Jun 2006 14:21:34 -0000	1.8
***************
*** 328,331 ****
--- 328,405 ----
            exons.each(&x)
          end
+ 
+         #--
+         # methods described in the BLAT FAQ at the UCSC genome browser.
+         # (http://genome.ucsc.edu/FAQ/FAQblat#blat5)
+         #++
+ 
+         # Calculates the pslCalcMilliBad value defined in the
+         # BLAT FAQ (http://genome.ucsc.edu/FAQ/FAQblat#blat5).
+         #
+         # The algorithm is taken from the BLAT FAQ
+         # (http://genome.ucsc.edu/FAQ/FAQblat#blat5).
+         def milli_bad
+           w = (self.protein? ? 3 : 1)
+           qalen = w * (self.query.end - self.query.start)
+           talen = self.target.end - self.target.start
+           alen = (if qalen < talen then qalen; else talen; end)
+           return 0 if alen <= 0
+           d = qalen - talen
+           d = 0 if d < 0
+           total = w * (self.match + self.rep_match + self.mismatch)
+           return 0 if total == 0
+           return (1000 * (self.mismatch * w + self.query.gap_count +
+                             (3 * Math.log(1 + d)).round) / total)
+         end
+ 
+         # Calculates the percent identity compatible with the BLAT web server
+         # as described in the BLAT FAQ
+         # (http://genome.ucsc.edu/FAQ/FAQblat#blat5).
+         #
+         # The algorithm is taken from the BLAT FAQ
+         # (http://genome.ucsc.edu/FAQ/FAQblat#blat5).
+         def percent_identity
+           100.0 - self.milli_bad * 0.1
+         end
+ 
+         # When the output data comes from the protein query, returns true.
+         # Otherwise (nucleotide query), returns false.
+         # It returns nil if this cannot be determined.
+         #
+         # The algorithm is taken from the BLAT FAQ
+         # (http://genome.ucsc.edu/FAQ/FAQblat#blat5).
+         def protein?
+           return nil if self.block_sizes.empty?
+           case self.strand
+           when '+'
+             if self.target.end == self.target.starts[-1] +
+                 3 * self.block_sizes[-1] then
+               true
+             else
+               false
+             end
+           when '-'
+             if self.target.start == self.target.size -
+                 self.target.starts[-1] + 3 * self.block_sizes[-1] then
+               true
+             else
+               false
+             end
+           else
+             nil
+           end
+         end
+ 
+         # Calculates the score compatible with the BLAT web server
+         # as described in the BLAT FAQ
+         # (http://genome.ucsc.edu/FAQ/FAQblat#blat5).
+         #
+         # The algorithm is taken from the BLAT FAQ
+         # (http://genome.ucsc.edu/FAQ/FAQblat#blat5).
+         def score
+           w = (self.protein? ? 3 : 1)
+           w * (self.match + (self.rep_match >> 1)) -
+             w * self.mismatch - self.query.gap_count - self.target.gap_count
+         end
        end #class Hit
  


From ngoto at dev.open-bio.org  Tue Jun 20 10:34:40 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Tue, 20 Jun 2006 14:34:40 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/blat report.rb,1.8,1.9
Message-ID: <200606201434.k5KEYeDQ001282@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl/blat
In directory dev.open-bio.org:/tmp/cvs-serv1262

Modified Files:
	report.rb 
Log Message:
Changed some documents.
Reference: http://genome.ucsc.edu/goldenPath/help/blatSpec.html


Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blat/report.rb,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** report.rb	20 Jun 2006 14:21:34 -0000	1.8
--- report.rb	20 Jun 2006 14:34:38 -0000	1.9
***************
*** 21,25 ****
  #   Genome Research, 12, 656--664, 2002.
  #   http://www.genome.org/cgi/content/abstract/12/4/656
! # 
  
  require 'bio'
--- 21,25 ----
  #   Genome Research, 12, 656--664, 2002.
  #   http://www.genome.org/cgi/content/abstract/12/4/656
! # * http://genome.ucsc.edu/goldenPath/help/blatSpec.html
  
  require 'bio'
***************
*** 262,268 ****
          # Mismatch nucleotides.
          def mismatch;    @data[1].to_i;  end
!         # rep. match (???)
          def rep_match;   @data[2].to_i;  end
!         # N's (???)
          def n_s;         @data[3].to_i;  end
  
--- 262,272 ----
          # Mismatch nucleotides.
          def mismatch;    @data[1].to_i;  end
! 
!         # "rep. match".
!         # Number of bases that match but are part of repeats.
!         # Note that current version of BLAT always set 0.
          def rep_match;   @data[2].to_i;  end
! 
!         # "N's". Number of 'N' bases.
          def n_s;         @data[3].to_i;  end
  


From ngoto at dev.open-bio.org  Thu Jun 22 10:32:49 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Thu, 22 Jun 2006 14:32:49 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/io flatfile.rb,1.50,1.51
Message-ID: <200606221432.k5MEWnV4007918@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/io
In directory dev.open-bio.org:/tmp/cvs-serv7898/lib/bio/io

Modified Files:
	flatfile.rb 
Log Message:
Fixed: failed to autodetect psLayout version 4 (Bio::BLAT::Report)


Index: flatfile.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/flatfile.rb,v
retrieving revision 1.50
retrieving revision 1.51
diff -C2 -d -r1.50 -r1.51
*** flatfile.rb	12 Jun 2006 10:35:42 -0000	1.50
--- flatfile.rb	22 Jun 2006 14:32:47 -0000	1.51
***************
*** 1196,1200 ****
  
            blat   = RuleRegexp[ 'Bio::Blat::Report',
!             /^psLayout version \d+\s*$/ ],
            spidey = RuleRegexp[ 'Bio::Spidey::Report',
              /^\-\-SPIDEY version .+\-\-$/ ],
--- 1196,1200 ----
  
            blat   = RuleRegexp[ 'Bio::Blat::Report',
!             /^psLayout version \d+/ ],
            spidey = RuleRegexp[ 'Bio::Spidey::Report',
              /^\-\-SPIDEY version .+\-\-$/ ],


From ngoto at dev.open-bio.org  Tue Jun 27 01:44:59 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Tue, 27 Jun 2006 05:44:59 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/sequence na.rb,1.3,1.4
Message-ID: <200606270544.k5R5ixTu007673@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/sequence
In directory dev.open-bio.org:/tmp/cvs-serv7649/lib/bio/sequence

Modified Files:
	na.rb 
Log Message:
Bio::Sequence::NA#gc_content, #at_content, #gc_skew, #at_skew
are newly added.
Bio::Sequence::NA#gc_percent are changed not to raise ZeroDivisionError
and returns 0 when given sequence is empty.


Index: na.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence/na.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** na.rb	26 Mar 2006 02:27:59 -0000	1.3
--- na.rb	27 Jun 2006 05:44:57 -0000	1.4
***************
*** 282,286 ****
  
    # Calculate the ratio of GC / ATGC bases as a percentage rounded to 
!   # the nearest whole number.
    #
    #   s = Bio::Sequence::NA.new('atggcgtga')
--- 282,286 ----
  
    # Calculate the ratio of GC / ATGC bases as a percentage rounded to 
!   # the nearest whole number. U is regarded as T.
    #
    #   s = Bio::Sequence::NA.new('atggcgtga')
***************
*** 292,299 ****
--- 292,356 ----
      at = count['a'] + count['t'] + count['u']
      gc = count['g'] + count['c']
+     return 0 if at + gc == 0
      gc = 100 * gc / (at + gc)
      return gc
    end
  
+   # Calculate the ratio of GC / ATGC bases. U is regarded as T.
+   #
+   #   s = Bio::Sequence::NA.new('atggcgtga')
+   #   puts s.gc_content                       #=> 0.555555555555556
+   # ---
+   # *Returns*:: Float
+   def gc_content
+     count = self.composition
+     at = count['a'] + count['t'] + count['u']
+     gc = count['g'] + count['c']
+     return 0.0 if at + gc == 0
+     return (gc.to_f / (at + gc).to_f)
+   end
+ 
+   # Calculate the ratio of AT / ATGC bases. U is regarded as T.
+   #
+   #   s = Bio::Sequence::NA.new('atggcgtga')
+   #   puts s.at_content                       #=> 0.444444444444444
+   # ---
+   # *Returns*:: Float
+   def at_content
+     count = self.composition
+     at = count['a'] + count['t'] + count['u']
+     gc = count['g'] + count['c']
+     return 0.0 if at + gc == 0
+     return (at.to_f / (at + gc).to_f)
+   end
+ 
+   # Calculate the ratio of (G - C) / (G + C) bases.
+   #
+   #   s = Bio::Sequence::NA.new('atggcgtga')
+   #   puts s.gc_skew                          #=> 0.6
+   # ---
+   # *Returns*:: Float
+   def gc_skew
+     count = self.composition
+     g = count['g']
+     c = count['c']
+     return 0.0 if g + c == 0
+     return ((g - c).to_f / (g + c).to_f)
+   end
+ 
+   # Calculate the ratio of (A - T) / (A + T) bases. U is regarded as T.
+   #
+   #   s = Bio::Sequence::NA.new('atgttgttgttc')
+   #   puts s.at_skew                          #=> -0.75
+   # ---
+   # *Returns*:: Float
+   def at_skew
+     count = self.composition
+     a = count['a']
+     t = count['t'] + count['u']
+     return 0.0 if a + t == 0
+     return ((a - t).to_f / (a + t).to_f)
+   end
+ 
    # Returns an alphabetically sorted array of any non-standard bases 
    # (other than 'atgcu').


From ngoto at dev.open-bio.org  Tue Jun 27 01:44:59 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Tue, 27 Jun 2006 05:44:59 +0000
Subject: [BioRuby-cvs] bioruby/test/unit/bio/sequence test_na.rb,1.1,1.2
Message-ID: <200606270544.k5R5ixYo007678@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/test/unit/bio/sequence
In directory dev.open-bio.org:/tmp/cvs-serv7649/test/unit/bio/sequence

Modified Files:
	test_na.rb 
Log Message:
Bio::Sequence::NA#gc_content, #at_content, #gc_skew, #at_skew
are newly added.
Bio::Sequence::NA#gc_percent are changed not to raise ZeroDivisionError
and returns 0 when given sequence is empty.


Index: test_na.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/sequence/test_na.rb,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** test_na.rb	8 Feb 2006 07:08:22 -0000	1.1
--- test_na.rb	27 Jun 2006 05:44:57 -0000	1.2
***************
*** 99,102 ****
--- 99,128 ----
      end
  
+     def test_gc_content
+       assert_in_delta(0.4, @obj.gc_content, Float::EPSILON)
+       @obj[0, 1] = 'g'
+       assert_in_delta(0.45, @obj.gc_content, Float::EPSILON)
+     end
+ 
+     def test_at_content
+       assert_in_delta(0.6, @obj.at_content, Float::EPSILON)
+       @obj[0, 1] = 'g'
+       assert_in_delta(0.55, @obj.at_content, Float::EPSILON)
+     end
+ 
+     def test_gc_skew
+       assert_in_delta(0.0, @obj.gc_skew, Float::EPSILON)
+       @obj[0, 1] = 'g'
+       assert_in_delta(1.0/9.0, @obj.gc_skew, Float::EPSILON)
+       @obj.gsub!(/a/, 'c')
+       assert_in_delta(-3.0/8.0, @obj.gc_skew, Float::EPSILON)
+     end
+ 
+     def test_at_skew
+       assert_in_delta(1.0/3.0, @obj.at_skew, Float::EPSILON)
+       @obj[0, 1] = 'g'
+       assert_in_delta(3.0/11.0, @obj.at_skew, Float::EPSILON)
+     end
+ 
      def test_iliegal_bases
        @obj[0, 1] = 'n'


From ngoto at dev.open-bio.org  Tue Jun 27 01:44:59 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Tue, 27 Jun 2006 05:44:59 +0000
Subject: [BioRuby-cvs] bioruby ChangeLog,1.52,1.53
Message-ID: <200606270544.k5R5ixDT007683@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby
In directory dev.open-bio.org:/tmp/cvs-serv7649

Modified Files:
	ChangeLog 
Log Message:
Bio::Sequence::NA#gc_content, #at_content, #gc_skew, #at_skew
are newly added.
Bio::Sequence::NA#gc_percent are changed not to raise ZeroDivisionError
and returns 0 when given sequence is empty.


Index: ChangeLog
===================================================================
RCS file: /home/repository/bioruby/bioruby/ChangeLog,v
retrieving revision 1.52
retrieving revision 1.53
diff -C2 -d -r1.52 -r1.53
*** ChangeLog	3 May 2006 00:07:58 -0000	1.52
--- ChangeLog	27 Jun 2006 05:44:57 -0000	1.53
***************
*** 1,2 ****
--- 1,11 ----
+ 2006-06-27  Naohisa Goto <ng at bioruby.org>
+ 
+         * lib/bio/sequence/na.rb
+ 
+           Bio::Sequence::NA#gc_content, #at_content, #gc_skew, #at_skew
+ 	  are newly added. Bio::Sequence::NA#gc_percent are changed
+ 	  not to raise ZeroDivisionError and returns 0 when given sequence
+ 	  is empty.
+ 
  2006-05-02  Mitsuteru Nakao <n at bioruby.org>
  


From aerts at dev.open-bio.org  Tue Jun 27 08:37:44 2006
From: aerts at dev.open-bio.org (Jan Aerts)
Date: Tue, 27 Jun 2006 12:37:44 +0000
Subject: [BioRuby-cvs] bioruby/test/unit/bio test_map.rb,1.2,1.3
Message-ID: <200606271237.k5RCbimc008730@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/test/unit/bio
In directory dev.open-bio.org:/tmp/cvs-serv8703/test/unit/bio

Modified Files:
	test_map.rb 
Log Message:
Removed Enumerable mixin from ActsLikeMap and ActsLikeMarker, because 'def each' would be ambiguous.
Included examples for using ActsLikeMap and ActsLikeMarker.


Index: test_map.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/test_map.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** test_map.rb	7 Jun 2006 12:56:29 -0000	1.2
--- test_map.rb	27 Jun 2006 12:37:42 -0000	1.3
***************
*** 6,10 ****
  # License::     Ruby's
  #
! # $Id$
  
  require 'pathname'
--- 6,10 ----
  # License::     Ruby's
  #
! # $Id:
  
  require 'pathname'
***************
*** 182,184 ****
--- 182,197 ----
      end
    end
+   
+   class Clone
+     include Bio::Map::ActsLikeMap
+     include Bio::Map::ActsLikeMarker
+     
+     def initialize(name)
+       @name = name
+       @mappings_as_map = Array.new
+       @mappings_as_marker = Array.new
+     end
+     attr_accessor :name, :mappings_as_map, :mappings_as_marker
+   end
+   
  end


From aerts at dev.open-bio.org  Tue Jun 27 08:37:44 2006
From: aerts at dev.open-bio.org (Jan Aerts)
Date: Tue, 27 Jun 2006 12:37:44 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio map.rb,1.6,1.7
Message-ID: <200606271237.k5RCbiae008725@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv8703/lib/bio

Modified Files:
	map.rb 
Log Message:
Removed Enumerable mixin from ActsLikeMap and ActsLikeMarker, because 'def each' would be ambiguous.
Included examples for using ActsLikeMap and ActsLikeMarker.


Index: map.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/map.rb,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** map.rb	7 Jun 2006 12:55:50 -0000	1.6
--- map.rb	27 Jun 2006 12:37:42 -0000	1.7
***************
*** 6,10 ****
  # Licence::     Ruby's
  #
! # $Id$
  require 'bio/location'
  
--- 6,10 ----
  # Licence::     Ruby's
  #
! # $Id:
  require 'bio/location'
  
***************
*** 65,74 ****
    #  puts "Does my_map2 contain marker3? => " + my_map2.contains_marker?(my_marker3).to_s
    #  
!   #  my_map1.sort.each do |mapping|
!   #    puts mapping.map.name + "\t" + mapping.marker.name + "\t" + mapping.location[0].from.to_s + ".." + mapping.location[-1].to.to_s
    #  end
!   #  puts my_map1.min.marker.name
!   #  my_map2.each do |mapping|
!   #    puts mapping.map.name + "\t" + mapping.marker.name + "\t" + mapping.location[0].from.to_s + ".." + mapping.location[-1].to.to_s
    #  end
    module Map
--- 65,74 ----
    #  puts "Does my_map2 contain marker3? => " + my_map2.contains_marker?(my_marker3).to_s
    #  
!   #  my_map1.mappings_as_map.sort.each do |mapping|
!   #    puts mapping.map.name + "\t" + mapping.marker.name + "\t" + mapping.location.from.to_s + ".." + mapping.location.to.to_s
    #  end
!   #  puts my_map1.mappings_as_map.min.marker.name
!   #  my_map2.mappings_as_map.each do |mapping|
!   #    puts mapping.map.name + "\t" + mapping.marker.name + "\t" + mapping.location.from.to_s + ".." + mapping.location.to.to_s
    #  end
    module Map
***************
*** 81,84 ****
--- 81,94 ----
    # 
    # Classes that include this mixin should provide an array property called mappings_as_map.
+   # For example:
+   #   class MyMapThing
+   #     include Bio::Map::ActsLikeMap
+   #     
+   #     def initialize (name)
+   #       @name = name
+   #       @mappings_as_maps = Array.new
+   #     end
+   #     attr_accessor :name, :mappings_as_map
+   #    end
      module ActsLikeMap
        include Enumerable
***************
*** 138,147 ****
        end
        
-       # Go through all Bio::Map::Mapping objects linked to this Bio::Map::SimpleMap.
-       def each
-         self.mappings_as_map.each do |mapping|
-           yield mapping
-         end
-       end
      end #ActsLikeMap
  
--- 148,151 ----
***************
*** 154,157 ****
--- 158,171 ----
      # 
      # Classes that include this mixin should provide an array property called mappings_as_marker.
+     # For example:
+     #   class MyMarkerThing
+     #     include Bio::Map::ActsLikeMarker
+     #     
+     #     def initialize (name)
+     #       @name = name
+     #       @mappings_as_marker = Array.new
+     #     end
+     #     attr_accessor :name, :mappings_as_marker
+     #    end
      module ActsLikeMarker
        include Enumerable
***************
*** 189,199 ****
          end
        end
- 
-       # Go through all Mapping objects linked to this marker.
-       def each
-         self.mappings_as_marker.each do |mapping|
-           yield mapping
-         end
-       end
        
        # Check whether this marker is mapped to a given Bio::Map::SimpleMap.
--- 203,206 ----
***************
*** 238,241 ****
--- 245,249 ----
        end
        
+ 
      end #ActsLikeMarker
  	  
***************
*** 253,257 ****
        # * _marker_: a Bio::Map::Marker object
        # * _location_: a Bio::Locations object
- 
        def initialize (map, marker, location = nil)
          @map, @marker, @location = map, marker, location
--- 261,264 ----
***************
*** 259,280 ****
        attr_accessor :map, :marker, :location
        
! #       # Compares the location of this mapping to another mapping.
! #       # ---
! #       # *Arguments*:
! #       # * other_mapping: Bio::Map::Mapping object
! #       # *Returns*::
! #       # * 1 if self < other location
! #       # * -1 if self > other location
! #       # * 0 if both location are the same
! #       # * nil if the argument is not a Bio::Location object
! #       def <=>(other)
! #         unless other.kind_of?(Bio::Map::Mapping)
! #           raise "[Error] markers are not comparable"
! #         end
! #         unless @map.equal?(other.map)
! #           raise "[Error] maps have to be the same"
! #         end
! #         return self.location<=>(other.location) # FIXME: no <=>-method in Bio::Locations
! #       end
      end # Mapping
      
--- 266,288 ----
        attr_accessor :map, :marker, :location
        
!       # Compares the location of this mapping to another mapping.
!       # ---
!       # *Arguments*:
!       # * other_mapping: Bio::Map::Mapping object
!       # *Returns*::
!       # * 1 if self < other location
!       # * -1 if self > other location
!       # * 0 if both location are the same
!       # * nil if the argument is not a Bio::Location object
!       def <=>(other)
!         unless other.kind_of?(Bio::Map::Mapping)
!           raise "[Error] markers are not comparable"
!         end
! 	    unless @map.equal?(other.map)
!           raise "[Error] maps have to be the same"
!         end
! 
!         return self.location.<=>(other.location)
!       end
      end # Mapping
      


From aerts at dev.open-bio.org  Tue Jun 27 08:40:17 2006
From: aerts at dev.open-bio.org (Jan Aerts)
Date: Tue, 27 Jun 2006 12:40:17 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio map.rb,1.7,1.8
Message-ID: <200606271240.k5RCeHJA008800@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv8780/lib/bio

Modified Files:
	map.rb 
Log Message:
Forgot to remove reference to Enumerable.


Index: map.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/map.rb,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** map.rb	27 Jun 2006 12:37:42 -0000	1.7
--- map.rb	27 Jun 2006 12:40:15 -0000	1.8
***************
*** 6,10 ****
  # Licence::     Ruby's
  #
! # $Id:
  require 'bio/location'
  
--- 6,10 ----
  # Licence::     Ruby's
  #
! # $Id$
  require 'bio/location'
  
***************
*** 92,97 ****
    #    end
      module ActsLikeMap
-       include Enumerable
-       
        # = DESCRIPTION
        # Adds a Bio::Map::Mappings object to its array of mappings.
--- 92,95 ----
***************
*** 169,174 ****
      #    end
      module ActsLikeMarker
-       include Enumerable
-       
        # = DESCRIPTION
        # Adds a Bio::Map::Mappings object to its array of mappings.
--- 167,170 ----


From ngoto at dev.open-bio.org  Tue Jun 27 10:23:47 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Tue, 27 Jun 2006 14:23:47 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/db/pdb pdb.rb,1.15,1.16
Message-ID: <200606271423.k5RENlQb009267@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/db/pdb
In directory dev.open-bio.org:/tmp/cvs-serv9227/lib/bio/db/pdb

Modified Files:
	pdb.rb 
Log Message:
Bio::PDB::ATOM#name, #resName, #iCode, #chaarge are changed to be strippedi
when initializing.
Bio::PDB::ATOM#segID is changed to be right-stripped when initializing.
Bio::PDB::ATOM#element is changed to be left-stripped when initializing.
(Because Bio::PDB::HETATM inherits Bio::PDB::ATOM, Bio::PDB::HETATM is
also subject to the changes.)


Index: pdb.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb/pdb.rb,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** pdb.rb	20 Feb 2006 13:00:43 -0000	1.15
--- pdb.rb	27 Jun 2006 14:23:45 -0000	1.16
***************
*** 993,1002 ****
            return self if @parsed
            self.serial     = @str[6..10].to_i
!           self.name       = @str[12..15]
            self.altLoc     = @str[16..16]
!           self.resName    = @str[17..19].rstrip
            self.chainID    = @str[21..21]
            self.resSeq     = @str[22..25].to_i
!           self.iCode      = @str[26..26]
            self.x          = @str[30..37].to_f
            self.y          = @str[38..45].to_f
--- 993,1002 ----
            return self if @parsed
            self.serial     = @str[6..10].to_i
!           self.name       = @str[12..15].strip
            self.altLoc     = @str[16..16]
!           self.resName    = @str[17..19].strip
            self.chainID    = @str[21..21]
            self.resSeq     = @str[22..25].to_i
!           self.iCode      = @str[26..26].strip
            self.x          = @str[30..37].to_f
            self.y          = @str[38..45].to_f
***************
*** 1004,1010 ****
            self.occupancy  = @str[54..59].to_f
            self.tempFactor = @str[60..65].to_f
!           self.segID      = @str[72..75]
!           self.element    = @str[76..77]
!           self.charge     = @str[78..79]
            @parsed = true
            self
--- 1004,1010 ----
            self.occupancy  = @str[54..59].to_f
            self.tempFactor = @str[60..65].to_f
!           self.segID      = @str[72..75].to_s.rstrip
!           self.element    = @str[76..77].to_s.lstrip
!           self.charge     = @str[78..79].to_s.strip
            @parsed = true
            self
***************
*** 1012,1019 ****
  
          def to_s
            sprintf("%-6s%5d %-4s%-1s%3s %-1s%4d%-1s   %8.3f%8.3f%8.3f%6.2f%6.2f      %-4s%2s%-2s\n",
                    self.record_name,
                    self.serial, 
!                   self.name,
                    self.altLoc,
                    self.resName,
--- 1012,1024 ----
  
          def to_s
+           atomname = self.name.to_s
+           elem = self.element.to_s.strip
+           if elem.length == 1 and atomname.lstrip[0, 1] == elem then
+             atomname = ' ' + atomname
+           end
            sprintf("%-6s%5d %-4s%-1s%3s %-1s%4d%-1s   %8.3f%8.3f%8.3f%6.2f%6.2f      %-4s%2s%-2s\n",
                    self.record_name,
                    self.serial, 
!                   atomname,
                    self.altLoc,
                    self.resName,


From ngoto at dev.open-bio.org  Tue Jun 27 10:25:42 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Tue, 27 Jun 2006 14:25:42 +0000
Subject: [BioRuby-cvs] bioruby/test/unit/bio/db/pdb test_pdb.rb,1.1,1.2
Message-ID: <200606271425.k5REPgfp009296@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/test/unit/bio/db/pdb
In directory dev.open-bio.org:/tmp/cvs-serv9276/test/unit/bio/db/pdb

Modified Files:
	test_pdb.rb 
Log Message:
* License is changed to Ruby's.
* Follow changes to pdb.rb (as is nearly the same behavior as bioruby-0.6.4).


Index: test_pdb.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/db/pdb/test_pdb.rb,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** test_pdb.rb	26 Jan 2006 16:06:03 -0000	1.1
--- test_pdb.rb	27 Jun 2006 14:25:40 -0000	1.2
***************
*** 5,29 ****
  #             Naohisa Goto <ng at bioruby.org>
  #
! # License:: LGPL
  #
  #  $Id$
  #
- #--
- #  This library is free software; you can redistribute it and/or
- #  modify it under the terms of the GNU Lesser General Public
- #  License as published by the Free Software Foundation; either
- #  version 2 of the License, or (at your option) any later version.
- #
- #  This library is distributed in the hope that it will be useful,
- #  but WITHOUT ANY WARRANTY; without even the implied warranty of
- #  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- #  Lesser General Public License for more details.
- #
- #  You should have received a copy of the GNU Lesser General Public
- #  License along with this library; if not, write to the Free Software
- #  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
- #++
- #
- #
  
  require 'pathname'
--- 5,12 ----
  #             Naohisa Goto <ng at bioruby.org>
  #
! # License:: Ruby's
  #
  #  $Id$
  #
  
  require 'pathname'
***************
*** 58,62 ****
  
        def test_name
!         assert_equal(' CG2', @atom.name)
        end
  
--- 41,45 ----
  
        def test_name
!         assert_equal('CG2', @atom.name)
        end
  
***************
*** 78,82 ****
  
        def test_iCode
!         assert_equal(' ', @atom.iCode)
        end
  
--- 61,65 ----
  
        def test_iCode
!         assert_equal('', @atom.iCode)
        end
  
***************
*** 102,114 ****
  
        def test_segID
!         assert_equal('A1  ', @atom.segID)
        end
  
        def test_element
!         assert_equal(' C', @atom.element)
        end
  
        def test_charge
!         assert_equal('  ', @atom.charge)
        end
  
--- 85,97 ----
  
        def test_segID
!         assert_equal('A1', @atom.segID)
        end
  
        def test_element
!         assert_equal('C', @atom.element)
        end
  
        def test_charge
!         assert_equal('', @atom.charge)
        end
  


From ngoto at dev.open-bio.org  Tue Jun 27 11:17:09 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Tue, 27 Jun 2006 15:17:09 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/blat report.rb,1.9,1.10
Message-ID: <200606271517.k5RFH9w8009506@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl/blat
In directory dev.open-bio.org:/tmp/cvs-serv9484/lib/bio/appl/blat

Modified Files:
	report.rb 
Log Message:
changed documents


Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blat/report.rb,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** report.rb	20 Jun 2006 14:34:38 -0000	1.9
--- report.rb	27 Jun 2006 15:17:07 -0000	1.10
***************
*** 34,38 ****
      # On the other hand, in many other homology search programs,
      # the start position of a sequence is numbered as 1.
!     # To keep compatibility, the BLAT parser adds 1 to every position number.
      #
      # Note that Bio::Blat::Report#query_def, #query_id, #query_len  methods
--- 34,39 ----
      # On the other hand, in many other homology search programs,
      # the start position of a sequence is numbered as 1.
!     # To keep compatibility, the BLAT parser adds 1 to every position number
!     # except Bio::Blat::Report::Seqdesc and some Bio::Blat specific methods.
      #
      # Note that Bio::Blat::Report#query_def, #query_id, #query_len  methods
***************
*** 335,346 ****
          #--
          # methods described in the BLAT FAQ at the UCSC genome browser.
!         # (http://genome.ucsc.edu/FAQ/FAQblat#blat5)
          #++
  
          # Calculates the pslCalcMilliBad value defined in the
!         # BLAT FAQ (http://genome.ucsc.edu/FAQ/FAQblat#blat5).
          #
          # The algorithm is taken from the BLAT FAQ
!         # (http://genome.ucsc.edu/FAQ/FAQblat#blat5).
          def milli_bad
            w = (self.protein? ? 3 : 1)
--- 336,347 ----
          #--
          # methods described in the BLAT FAQ at the UCSC genome browser.
!         # (http://genome.ucsc.edu/FAQ/FAQblat#blat4)
          #++
  
          # Calculates the pslCalcMilliBad value defined in the
!         # BLAT FAQ (http://genome.ucsc.edu/FAQ/FAQblat#blat4).
          #
          # The algorithm is taken from the BLAT FAQ
!         # (http://genome.ucsc.edu/FAQ/FAQblat#blat4).
          def milli_bad
            w = (self.protein? ? 3 : 1)
***************
*** 359,366 ****
          # Calculates the percent identity compatible with the BLAT web server
          # as described in the BLAT FAQ
!         # (http://genome.ucsc.edu/FAQ/FAQblat#blat5).
          #
          # The algorithm is taken from the BLAT FAQ
!         # (http://genome.ucsc.edu/FAQ/FAQblat#blat5).
          def percent_identity
            100.0 - self.milli_bad * 0.1
--- 360,367 ----
          # Calculates the percent identity compatible with the BLAT web server
          # as described in the BLAT FAQ
!         # (http://genome.ucsc.edu/FAQ/FAQblat#blat4).
          #
          # The algorithm is taken from the BLAT FAQ
!         # (http://genome.ucsc.edu/FAQ/FAQblat#blat4).
          def percent_identity
            100.0 - self.milli_bad * 0.1
***************
*** 372,376 ****
          #
          # The algorithm is taken from the BLAT FAQ
!         # (http://genome.ucsc.edu/FAQ/FAQblat#blat5).
          def protein?
            return nil if self.block_sizes.empty?
--- 373,377 ----
          #
          # The algorithm is taken from the BLAT FAQ
!         # (http://genome.ucsc.edu/FAQ/FAQblat#blat4).
          def protein?
            return nil if self.block_sizes.empty?
***************
*** 397,404 ****
          # Calculates the score compatible with the BLAT web server
          # as described in the BLAT FAQ
!         # (http://genome.ucsc.edu/FAQ/FAQblat#blat5).
          #
          # The algorithm is taken from the BLAT FAQ
!         # (http://genome.ucsc.edu/FAQ/FAQblat#blat5).
          def score
            w = (self.protein? ? 3 : 1)
--- 398,405 ----
          # Calculates the score compatible with the BLAT web server
          # as described in the BLAT FAQ
!         # (http://genome.ucsc.edu/FAQ/FAQblat#blat4).
          #
          # The algorithm is taken from the BLAT FAQ
!         # (http://genome.ucsc.edu/FAQ/FAQblat#blat4).
          def score
            w = (self.protein? ? 3 : 1)


From ngoto at dev.open-bio.org  Wed Jun 28 09:43:33 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Wed, 28 Jun 2006 13:43:33 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/blat report.rb,1.10,1.11
Message-ID: <200606281343.k5SDhXq7013712@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl/blat
In directory dev.open-bio.org:/tmp/cvs-serv13692/lib/bio/appl/blat

Modified Files:
	report.rb 
Log Message:
* Fixed a bug in Bio::Blat::Report::Hit#protein?.
* Fixed: when protein query and nucleotide database, HSPs are incorrect.


Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blat/report.rb,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** report.rb	27 Jun 2006 15:17:07 -0000	1.10
--- report.rb	28 Jun 2006 13:43:31 -0000	1.11
***************
*** 140,149 ****
          # It is designed to be called internally from Bio::Blat::Report class.
          # Users shall not use it directly.
!         def initialize(query_len, strand,
!                        blksize, qstart, tstart, qseq, tseq)
            @blocksize  = blksize
            @qseq       = qseq
            @hseq       = hseq
            @hit_strand   = 'plus'
            case strand
            when '-'
--- 140,151 ----
          # It is designed to be called internally from Bio::Blat::Report class.
          # Users shall not use it directly.
!         def initialize(query_len, target_len, strand,
!                        blksize, qstart, tstart, qseq, tseq,
!                        protein_flag)
            @blocksize  = blksize
            @qseq       = qseq
            @hseq       = hseq
            @hit_strand   = 'plus'
+           w = (protein_flag ? 3 : 1) # 3 means query=protein target=dna
            case strand
            when '-'
***************
*** 156,161 ****
              # we add 1 to each position number.
              @hit_from   = tstart + 1
!             @hit_to     = tstart + blksize # - 1 + 1
!           else #when '+'
              @query_strand = 'plus'
              # To keep compatibility with other homology search programs,
--- 158,174 ----
              # we add 1 to each position number.
              @hit_from   = tstart + 1
!             @hit_to     = tstart + blksize * w # - 1 + 1
!           when '+-'
!             # hit is minus strand
!             @query_strand = 'plus'
!             @hit_strand = 'minus'
!             # To keep compatibility, with other homology search programs,
!             # we add 1 to each position number.
!             @query_from   = qstart + 1
!             @query_to     = qstart + blksize # - 1 + 1
!             # convert positions
!             @hit_from     = target_len - tstart
!             @hit_to       = target_len - tstart - blksize * w + 1
!           else #when '+', '++'
              @query_strand = 'plus'
              # To keep compatibility with other homology search programs,
***************
*** 164,168 ****
              @query_to   = qstart + blksize # - 1 + 1
              @hit_from   = tstart + 1
!             @hit_to     = tstart + blksize # - 1 + 1
            end
          end
--- 177,181 ----
              @query_to   = qstart + blksize # - 1 + 1
              @hit_from   = tstart + 1
!             @hit_to     = tstart + blksize * w # - 1 + 1
            end
          end
***************
*** 298,304 ****
              qseqs = query.seqs
              tseqs = target.seqs
              @blocks = (0...block_count).collect do |i|
!               SegmentPair.new(query.size, strand, bs[i],
!                               qst[i], tst[i], qseqs[i], tseqs[i])
              end
            end
--- 311,319 ----
              qseqs = query.seqs
              tseqs = target.seqs
+             pflag = self.protein?
              @blocks = (0...block_count).collect do |i|
!               SegmentPair.new(query.size, target.size, strand, bs[i],
!                               qst[i], tst[i], qseqs[i], tseqs[i],
!                               pflag)
              end
            end
***************
*** 374,380 ****
          # The algorithm is taken from the BLAT FAQ
          # (http://genome.ucsc.edu/FAQ/FAQblat#blat4).
          def protein?
            return nil if self.block_sizes.empty?
!           case self.strand
            when '+'
              if self.target.end == self.target.starts[-1] +
--- 389,398 ----
          # The algorithm is taken from the BLAT FAQ
          # (http://genome.ucsc.edu/FAQ/FAQblat#blat4).
+         #
+         # Note: It seems that it returns true only when protein query
+         # with nucleotide database (blat options: -q=prot -t=dnax).
          def protein?
            return nil if self.block_sizes.empty?
!           case self.strand[1,1]
            when '+'
              if self.target.end == self.target.starts[-1] +
***************
*** 386,390 ****
            when '-'
              if self.target.start == self.target.size -
!                 self.target.starts[-1] + 3 * self.block_sizes[-1] then
                true
              else
--- 404,408 ----
            when '-'
              if self.target.start == self.target.size -
!                 self.target.starts[-1] - 3 * self.block_sizes[-1] then
                true
              else


From ngoto at dev.open-bio.org  Thu Jun 29 07:54:35 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Thu, 29 Jun 2006 11:54:35 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/blat report.rb,1.11,1.12
Message-ID: <200606291154.k5TBsZud023085@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl/blat
In directory dev.open-bio.org:/tmp/cvs-serv23065/lib/bio/appl/blat

Modified Files:
	report.rb 
Log Message:
* psl without header is supported.
* New attribute ``psl_version'' is added.


Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blat/report.rb,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** report.rb	28 Jun 2006 13:43:31 -0000	1.11
--- report.rb	29 Jun 2006 11:54:33 -0000	1.12
***************
*** 59,62 ****
--- 59,67 ----
              @hits << Hit.new(line)
            else
+             # for headerless data
+             if /^\d/ =~ line then
+               flag = true
+               redo
+             end
              line = line.chomp
              if /\A\-+\s*\z/ =~ line
***************
*** 81,85 ****
        # Parses headers.
        def parse_header(ary)
!         ary.shift # first line is removed
          a0 = ary.collect { |x| x.split(/\t/) }
          k = []
--- 86,98 ----
        # Parses headers.
        def parse_header(ary)
!         while x = ary.shift
!           if /psLayout version (\S+)/ =~ x then
!             @psl_version = $1
!             break
!           elsif !(x.strip.empty?)
!             ary.unshift(x)
!             break
!           end
!         end
          a0 = ary.collect { |x| x.split(/\t/) }
          k = []
***************
*** 95,98 ****
--- 108,114 ----
        private :parse_header
  
+       # version of the psl format (String or nil).
+       attr_reader :psl_version
+ 
        # Bio::Blat::Report::SeqDesc stores sequence information of
        # query or subject of the BLAT report.


From nakao at dev.open-bio.org  Mon Jun  5 02:52:01 2006
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Mon, 05 Jun 2006 02:52:01 +0000
Subject: [BioRuby-cvs] bioruby/test/unit/bio/io test_soapwsdl.rb,1.1,1.2
Message-ID: <200606050252.k552q1l2022218@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/test/unit/bio/io
In directory dev.open-bio.org:/tmp/cvs-serv22198/test/unit/bio/io

Modified Files:
	test_soapwsdl.rb 
Log Message:
* updated test_methods for recently added list_methods method in 
  lib/bio/io/soapwsdl.rb.


Index: test_soapwsdl.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/io/test_soapwsdl.rb,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** test_soapwsdl.rb	18 Dec 2005 17:09:53 -0000	1.1
--- test_soapwsdl.rb	5 Jun 2006 02:51:59 -0000	1.2
***************
*** 2,20 ****
  # test/unit/bio/io/test_soapwsdl.rb - Unit test for SOAP/WSDL
  #
! #   Copyright (C) 2005 Mitsuteru Nakao <n at bioruby.org>
! #
! #  This library is free software; you can redistribute it and/or
! #  modify it under the terms of the GNU Lesser General Public
! #  License as published by the Free Software Foundation; either
! #  version 2 of the License, or (at your option) any later version.
! #
! #  This library is distributed in the hope that it will be useful,
! #  but WITHOUT ANY WARRANTY; without even the implied warranty of
! #  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
! #  Lesser General Public License for more details.
! #
! #  You should have received a copy of the GNU Lesser General Public
! #  License along with this library; if not, write to the Free Software
! #  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
  #
  #  $Id$ 
--- 2,7 ----
  # test/unit/bio/io/test_soapwsdl.rb - Unit test for SOAP/WSDL
  #
! # Copytight::   Copyright (C) 2005 Mitsuteru Nakao <n at bioruby.org>
! # License::     Ruby's
  #
  #  $Id$ 
***************
*** 38,42 ****
  
    def test_methods
!     methods = ['wsdl', 'wsdl=', 'log', 'log=']
      assert_equal(methods.sort, (@obj.instance_methods - Object.methods).sort)
    end
--- 25,29 ----
  
    def test_methods
!     methods = ['list_methods','wsdl', 'wsdl=', 'log', 'log=']
      assert_equal(methods.sort, (@obj.instance_methods - Object.methods).sort)
    end



From nakao at dev.open-bio.org  Mon Jun  5 02:54:44 2006
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Mon, 05 Jun 2006 02:54:44 +0000
Subject: [BioRuby-cvs] bioruby/test/unit/bio/appl test_pts1.rb,1.1,1.2
Message-ID: <200606050254.k552sikS022267@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/test/unit/bio/appl
In directory dev.open-bio.org:/tmp/cvs-serv22247/test/unit/bio/appl

Modified Files:
	test_pts1.rb 
Log Message:
* added test_entry_id in TestPTS1Report class.


Index: test_pts1.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/appl/test_pts1.rb,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** test_pts1.rb	2 May 2006 10:29:19 -0000	1.1
--- test_pts1.rb	5 Jun 2006 02:54:42 -0000	1.2
***************
*** 106,109 ****
--- 106,113 ----
      end
  
+     def test_entry_id
+       assert_equal("hoge", @report.entry_id)
+     end
+ 
      def test_prediction
        assert_equal("Targeted", @report.prediction)



From nakao at dev.open-bio.org  Mon Jun  5 02:55:53 2006
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Mon, 05 Jun 2006 02:55:53 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl pts1.rb,1.2,1.3
Message-ID: <200606050255.k552trVs022316@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl
In directory dev.open-bio.org:/tmp/cvs-serv22296/lib/bio/appl

Modified Files:
	pts1.rb 
Log Message:
* added Bio::PTS1::Report#entry_id.


Index: pts1.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/pts1.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** pts1.rb	9 May 2006 08:18:49 -0000	1.2
--- pts1.rb	5 Jun 2006 02:55:51 -0000	1.3
***************
*** 175,178 ****
--- 175,181 ----
    class Report
  
+     # Query sequence name.
+     attr_reader :entry_id
+ 
      # Amino acids subsequence at C-terminal region.
      attr_reader :cterm
***************
*** 229,232 ****
--- 232,237 ----
        @output.each do |line|
          case line
+         when /Name<\/td><td>(\S.+)<\/td><\/tr>/
+           @entry_id = $1
          when /C-terminus<\/td><td>(\w+)<\/td>/
            @cterm = $1



From aerts at dev.open-bio.org  Wed Jun  7 12:55:52 2006
From: aerts at dev.open-bio.org (Jan Aerts)
Date: Wed, 07 Jun 2006 12:55:52 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio map.rb,1.5,1.6
Message-ID: <200606071255.k57CtqFA003705@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv3575

Modified Files:
	map.rb 
Log Message:
* Added Bio::Locations#equal? method. (Should be moved to location.rb, if approved.)
* Methods add_mapping_to_marker and add_mapping_to_map renamed to
  add_mapping_as_map and add_mapping_as_marker, respectively, to lessen the
  confusion of what is mapped to what.
* When adding a new mapping to a map or marker, a check is done first to see
  if that mapping has been added before or not.
* New method: Bio::Map::ActsLikeMarker#positions_on(map)


Index: map.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/map.rb,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** map.rb	4 May 2006 18:41:08 -0000	1.5
--- map.rb	7 Jun 2006 12:55:50 -0000	1.6
***************
*** 6,12 ****
--- 6,28 ----
  # Licence::     Ruby's
  #
+ # $Id$
  require 'bio/location'
  
  module Bio
+ 
+   # Add a method to Bio::Locations class
+   class Locations
+     def equals?(other)
+       if ! other.kind_of?(Bio::Locations)
+         return nil
+       end
+       if self.sort == other.sort
+         return true
+       else
+         return false
+       end
+     end
+   end
+ 
    # = DESCRIPTION
    # The Bio::Module contains classes that describe mapping information and can
***************
*** 42,48 ****
    #  my_map2 = Bio::Map::SimpleMap.new('consensus', 'linkage', 'cM')
    #  
!   #  my_map1.add_mapping_to_marker(my_marker1, '17')
!   #  my_map1.add_mapping_to_marker(Bio::Map::Marker.new('marker2'), '5')
!   #  my_marker3.add_mapping_to_marker(my_map1, '9')
    #  
    #  puts "Does my_map1 contain marker3? => " + my_map1.contains_marker?(my_marker3).to_s
--- 58,64 ----
    #  my_map2 = Bio::Map::SimpleMap.new('consensus', 'linkage', 'cM')
    #  
!   #  my_map1.add_mapping_as_map(my_marker1, '17')
!   #  my_map1.add_mapping_as_map(Bio::Map::Marker.new('marker2'), '5')
!   #  my_marker3.add_mapping_as_marker(my_map1, '9')
    #  
    #  puts "Does my_map1 contain marker3? => " + my_map1.contains_marker?(my_marker3).to_s
***************
*** 50,63 ****
    #  
    #  my_map1.sort.each do |mapping|
!   #    puts mapping.map.name + "\t" + mapping.marker.name + "\t" + mapping.location.from.to_s + ".." + mapping.location.to.to_s
    #  end
    #  puts my_map1.min.marker.name
    #  my_map2.each do |mapping|
!   #    puts mapping.map.name + "\t" + mapping.marker.name + "\t" + mapping.location.from.to_s + ".." + mapping.location.to.to_s
    #  end
-   #
-   # = TODO
-   # Check if initialization of @mappings can be done in ActsLikeMap and
-   # ActsLikeMarker, instead of in the classes that include these modules.
    module Map
    # = DESCRIPTION
--- 66,75 ----
    #  
    #  my_map1.sort.each do |mapping|
!   #    puts mapping.map.name + "\t" + mapping.marker.name + "\t" + mapping.location[0].from.to_s + ".." + mapping.location[-1].to.to_s
    #  end
    #  puts my_map1.min.marker.name
    #  my_map2.each do |mapping|
!   #    puts mapping.map.name + "\t" + mapping.marker.name + "\t" + mapping.location[0].from.to_s + ".." + mapping.location[-1].to.to_s
    #  end
    module Map
    # = DESCRIPTION
***************
*** 67,72 ****
--- 79,87 ----
    # * check if a given marker is mapped to it
    # , and can be mixed into other classes (e.g. Bio::Map::SimpleMap)
+   # 
+   # Classes that include this mixin should provide an array property called mappings_as_map.
      module ActsLikeMap
        include Enumerable
+       
        # = DESCRIPTION
        # Adds a Bio::Map::Mappings object to its array of mappings.
***************
*** 74,78 ****
        # = USAGE
        #   # suppose we have a Bio::Map::SimpleMap object called my_map
!       #   my_map.add_mapping_to_marker(Bio::Map::Marker.new('marker_a'), '5')
        # ---
        # *Arguments*:
--- 89,93 ----
        # = USAGE
        #   # suppose we have a Bio::Map::SimpleMap object called my_map
!       #   my_map.add_mapping_as_map(Bio::Map::Marker.new('marker_a'), '5')
        # ---
        # *Arguments*:
***************
*** 80,91 ****
        # * _location_: location of mapping. Should be a _string_, not a _number_.
        # *Returns*:: itself
!       def add_mapping_to_marker(marker, location = nil)
          unless marker.class.include?(Bio::Map::ActsLikeMarker)
            raise "[Error] marker is not object that implements Bio::Map::ActsLikeMarker"
          end
!         my_mapping = Bio::Map::Mapping.new(self, marker, Bio::Location.new(location))
!         @mappings.push(my_mapping)
!         unless marker.mapped_to?(self)
!           marker.mappings.push(my_mapping)
          end
  
--- 95,117 ----
        # * _location_: location of mapping. Should be a _string_, not a _number_.
        # *Returns*:: itself
!       def add_mapping_as_map(marker, location = nil)
          unless marker.class.include?(Bio::Map::ActsLikeMarker)
            raise "[Error] marker is not object that implements Bio::Map::ActsLikeMarker"
          end
!         my_mapping = ( location.nil? ) ? Bio::Map::Mapping.new(self, marker, nil) : Bio::Map::Mapping.new(self, marker, Bio::Locations.new(location))
!         if ! marker.mapped_to?(self)
!           self.mappings_as_map.push(my_mapping)
!           marker.mappings_as_marker.push(my_mapping)
!         else
!           already_mapped = false
!           marker.positions_on(self).each do |loc|
!             if loc.equals?(Bio::Locations.new(location))
!               already_mapped = true
!             end
!           end
!           if ! already_mapped
!             self.mappings_as_map.push(my_mapping)
!             marker.mappings_as_marker.push(my_mapping)
!           end
          end
  
***************
*** 103,107 ****
          end
          contains = false
!         @mappings.each do |mapping|
            if mapping.marker == marker
              contains = true
--- 129,133 ----
          end
          contains = false
!         self.mappings_as_map.each do |mapping|
            if mapping.marker == marker
              contains = true
***************
*** 114,118 ****
        # Go through all Bio::Map::Mapping objects linked to this Bio::Map::SimpleMap.
        def each
!         @mappings.each do |mapping|
            yield mapping
          end
--- 140,144 ----
        # Go through all Bio::Map::Mapping objects linked to this Bio::Map::SimpleMap.
        def each
!         self.mappings_as_map.each do |mapping|
            yield mapping
          end
***************
*** 126,129 ****
--- 152,157 ----
      # * check if it's mapped to a given map
      # , and can be mixed into other classes (e.g. Bio::Map::Marker)
+     # 
+     # Classes that include this mixin should provide an array property called mappings_as_marker.
      module ActsLikeMarker
        include Enumerable
***************
*** 134,138 ****
        # = USAGE
        #   # suppose we have a Bio::Map::Marker object called marker_a
!       #   marker_a.add_mapping_to_map(Bio::Map::SimpleMap.new('my_map'), '5')
        # ---
        # *Arguments*:
--- 162,166 ----
        # = USAGE
        #   # suppose we have a Bio::Map::Marker object called marker_a
!       #   marker_a.add_mapping_as_marker(Bio::Map::SimpleMap.new('my_map'), '5')
        # ---
        # *Arguments*:
***************
*** 140,151 ****
        # * _location_: location of mapping. Should be a _string_, not a _number_.
        # *Returns*:: itself
!       def add_mapping_to_map(map, location = nil)
          unless map.class.include?(Bio::Map::ActsLikeMap)
            raise "[Error] map is not object that implements Bio::Map::ActsLikeMap"
          end
!         my_mapping = Bio::Map::Mapping.new(map, self, Bio::Location.new(location))
!         @mappings.push(my_mapping)
!         unless map.contains_marker?(self)
!           map.mappings.push(my_mapping)
          end
        end
--- 168,197 ----
        # * _location_: location of mapping. Should be a _string_, not a _number_.
        # *Returns*:: itself
!       def add_mapping_as_marker(map, location = nil)
          unless map.class.include?(Bio::Map::ActsLikeMap)
            raise "[Error] map is not object that implements Bio::Map::ActsLikeMap"
          end
!         my_mapping = (location.nil?) ? Bio::Map::Mappings.new(map, self, nil) : Bio::Map::Mapping.new(map, self, Bio::Locations.new(location))
!         if ! self.mapped_to?(map)
!           self.mappings_as_marker.push(my_mapping)
!           map.mappings_as_map.push(my_mapping)
!         else
!           already_mapped = false
!           self.positions_on(map).each do |loc|
!             if loc.equals?(Bio::Locations.new(location))
!               already_mapped = true
!             end
!           end
!           if ! already_mapped
!             self.mappings_as_marker.push(my_mapping)
!             map.mappings_as_map.push(my_mapping)
!           end
!         end
!       end
! 
!       # Go through all Mapping objects linked to this marker.
!       def each
!         self.mappings_as_marker.each do |mapping|
!           yield mapping
          end
        end
***************
*** 160,166 ****
            raise "[Error] map is not object that implements Bio::Map::ActsLikeMap"
          end
! 				
          mapped = false
!         @mappings.each do |mapping|
            if mapping.map == map
              mapped = true
--- 206,212 ----
            raise "[Error] map is not object that implements Bio::Map::ActsLikeMap"
          end
! 		
          mapped = false
!         self.mappings_as_marker.each do |mapping|
            if mapping.map == map
              mapped = true
***************
*** 168,180 ****
            end
          end
          return mapped
        end
!       
!       # Go through all Mapping objects linked to this marker.
!       def each
!         @mappings.each do |mapping|
!           yield mapping
          end
        end
      end #ActsLikeMarker
  	  
--- 214,241 ----
            end
          end
+ 
          return mapped
        end
! 
!       # Return all positions of this marker on a given map.
!       # ---
!       # *Arguments*:
!       # * _map_: an object that mixes in Bio::Map::ActsLikeMap
!       # *Returns*:: array of Bio::Location objects
!       def positions_on(map)
!         unless map.class.include?(Bio::Map::ActsLikeMap)
!           raise "[Error] map is not object that implements Bio::Map::ActsLikeMap"
!         end
!         
!         positions = Array.new
!         self.mappings_as_marker.each do |mapping|
!           if mapping.map == map
!             positions.push(mapping.location)
!           end
          end
+         
+         return positions
        end
+       
      end #ActsLikeMarker
  	  
***************
*** 191,195 ****
        # * _map_: a Bio::Map::SimpleMap object
        # * _marker_: a Bio::Map::Marker object
!       # * _location_: a Bio::Location object
        def initialize (map, marker, location = nil)
          @map, @marker, @location = map, marker, location
--- 252,257 ----
        # * _map_: a Bio::Map::SimpleMap object
        # * _marker_: a Bio::Map::Marker object
!       # * _location_: a Bio::Locations object
! 
        def initialize (map, marker, location = nil)
          @map, @marker, @location = map, marker, location
***************
*** 197,219 ****
        attr_accessor :map, :marker, :location
        
!       # Compares the location of this mapping to another mapping.
!       # ---
!       # *Arguments*:
!       # * other_mapping: Bio::Map::Mapping object
!       # *Returns*::
!       # * 1 if self < other location
!       # * -1 if self > other location
!       # * 0 if both location are the same
!       # * nil if the argument is not a Bio::Location object
!       def <=>(other)
!         unless other.kind_of?(Bio::Map::Mapping)
!           raise "[Error] markers are not comparable"
!         end
! 	unless @map.equal?(other.map)
! 	  raise "[Error] maps have to be the same"
! 	end
! 
!         return self.location.<=>(other.location)
!       end
      end # Mapping
      
--- 259,280 ----
        attr_accessor :map, :marker, :location
        
! #       # Compares the location of this mapping to another mapping.
! #       # ---
! #       # *Arguments*:
! #       # * other_mapping: Bio::Map::Mapping object
! #       # *Returns*::
! #       # * 1 if self < other location
! #       # * -1 if self > other location
! #       # * 0 if both location are the same
! #       # * nil if the argument is not a Bio::Location object
! #       def <=>(other)
! #         unless other.kind_of?(Bio::Map::Mapping)
! #           raise "[Error] markers are not comparable"
! #         end
! #         unless @map.equal?(other.map)
! #           raise "[Error] maps have to be the same"
! #         end
! #         return self.location<=>(other.location) # FIXME: no <=>-method in Bio::Locations
! #       end
      end # Mapping
      
***************
*** 228,232 ****
      #   my_map1.add_marker(Bio::Map::Marker.new('marker_b', '5')
      class SimpleMap
!     include ActsLikeMap
      
        # Builds a new Bio::Map::SimpleMap object
--- 289,293 ----
      #   my_map1.add_marker(Bio::Map::Marker.new('marker_b', '5')
      class SimpleMap
!       include Bio::Map::ActsLikeMap
      
        # Builds a new Bio::Map::SimpleMap object
***************
*** 237,243 ****
        # * units: unit of the map (e.g. cM, cR, ...)
        # *Returns*:: new Bio::Map::SimpleMap object
!       def initialize (name = nil, type = nil, units = nil)
!         @name, @type, @units = name, type, units
!         @mappings = Array.new
        end
        
--- 298,304 ----
        # * units: unit of the map (e.g. cM, cR, ...)
        # *Returns*:: new Bio::Map::SimpleMap object
!       def initialize (name = nil, type = nil, length = nil, units = nil)
!         @name, @type, @length, @units = name, type, length, units
!         @mappings_as_map = Array.new
        end
        
***************
*** 247,256 ****
        # Type of the map
        attr_accessor :type
! 			
        # Units of the map
        attr_accessor :units
        
!       # Array of mappings for the map
!       attr_accessor :mappings
      end # SimpleMap
      
--- 308,321 ----
        # Type of the map
        attr_accessor :type
! 	
!       # Length of the map
!       attr_accessor :length
!       		
        # Units of the map
        attr_accessor :units
        
!       # Mappings
!       attr_accessor :mappings_as_map
!       
      end # SimpleMap
      
***************
*** 264,268 ****
      #   marker_b = Bio::Map::Marker.new('marker_b')
      class Marker
!       include ActsLikeMarker
        
        # Builds a new Bio::Map::Marker object
--- 329,333 ----
      #   marker_b = Bio::Map::Marker.new('marker_b')
      class Marker
!       include Bio::Map::ActsLikeMarker
        
        # Builds a new Bio::Map::Marker object
***************
*** 273,315 ****
        def initialize(name)
          @name = name
!         @mappings = Array.new
        end
  
        # Name of the marker
        attr_accessor :name
! 			
!       # Array of mappings for the marker
!       attr_accessor :mappings
      end # Marker
    end # Map
  end # Bio
- 
- if __FILE__ == $0
-   my_marker1 = Bio::Map::Marker.new('marker1')
- #  my_marker2 = Bio::Map::Marker.new('marker2')
-   my_marker3 = Bio::Map::Marker.new('marker3')
- 
-   my_map1 = Bio::Map::SimpleMap.new('RH_map_ABC (2006)', 'RH', 'cR')
-   my_map2 = Bio::Map::SimpleMap.new('consensus', 'linkage', 'cM')
- 
-   my_map1.add_mapping_to_marker(my_marker1, '17')
-   my_map1.add_mapping_to_marker(Bio::Map::Marker.new('marker2'), '5')
-   my_marker3.add_mapping_to_map(my_map1, '9')
- 
-   my_map2.add_mapping_to_marker(my_marker1, '57')
- 
-   puts "Does my_map1 contain marker3? => " + my_map1.contains_marker?(my_marker3).to_s
-   puts "Does my_map2 contain marker3? => " + my_map2.contains_marker?(my_marker3).to_s
- 
-   my_map1.sort.each do |mapping|
-     puts mapping.map.name + "\t" + mapping.marker.name + "\t" + mapping.location.from.to_s + ".." + mapping.location.to.to_s
-   end
-   puts my_map1.min.marker.name
- 
-   my_map2.each do |mapping|
-     puts mapping.map.name + "\t" + mapping.marker.name + "\t" + mapping.location.from.to_s + ".." + mapping.location.to.to_s
-   end
- 
- #  p my_map1.between?(my_mappable2,my_mappable3)
- #  p my_map1.between?(my_mappable,my_mappable2)
- end
--- 338,351 ----
        def initialize(name)
          @name = name
!         @mappings_as_marker = Array.new
        end
  
        # Name of the marker
        attr_accessor :name
!       
!       # Mappings
!       attr_accessor :mappings_as_marker
!       
      end # Marker
    end # Map
  end # Bio



From aerts at dev.open-bio.org  Wed Jun  7 12:56:31 2006
From: aerts at dev.open-bio.org (Jan Aerts)
Date: Wed, 07 Jun 2006 12:56:31 +0000
Subject: [BioRuby-cvs] bioruby/test/unit/bio test_map.rb,1.1,1.2
Message-ID: <200606071256.k57CuVZC003751@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/test/unit/bio
In directory dev.open-bio.org:/tmp/cvs-serv3723

Modified Files:
	test_map.rb 
Log Message:
Following changes in map.rb


Index: test_map.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/test_map.rb,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** test_map.rb	4 May 2006 16:19:52 -0000	1.1
--- test_map.rb	7 Jun 2006 12:56:29 -0000	1.2
***************
*** 5,8 ****
--- 5,10 ----
  #               Jan Aerts <jan.aerts at bbsrc.ac.uk>
  # License::     Ruby's
+ #
+ # $Id$
  
  require 'pathname'
***************
*** 14,102 ****
  
  module Bio
! 	class TestMapSimple < Test::Unit::TestCase
! 		def setup
! 			@marker1 = Bio::Map::Marker.new('marker1')
! 			@marker2 = Bio::Map::Marker.new('marker2')
! 			@map1 = Bio::Map::SimpleMap.new('map1', 'some_type', 'some_unit')
! 		end
  
! 		def test_attributes
! 			assert_equal("marker1", @marker1.name)
! 			assert_equal("marker2", @marker2.name)
! 			assert_equal([], @marker1.mappings)
! 			assert_equal([], @marker2.mappings)
! 			assert_equal("map1", @map1.name)
! 			assert_equal("some_unit", @map1.units)
! 			assert_equal("some_type", @map1.type)
! 			assert_equal([], @map1.mappings)
! 		end
! 	end
  
! 	class TestMapping < Test::Unit::TestCase
! 		def setup
! 			@marker1 = Bio::Map::Marker.new('marker1')
! 			@marker2 = Bio::Map::Marker.new('marker2')
! 			@map1 = Bio::Map::SimpleMap.new('map1', 'some_type', 'some_unit')
! 		end
  
! 		def test_add_mapping_to_marker
! 			@map1.add_mapping_to_marker(@marker2, '5')
! 			assert_equal(1, @map1.mappings.length)
! 			assert_equal(1, @marker2.mappings.length)
! 			assert_equal(0, @marker1.mappings.length)
! 			assert_kind_of(Bio::Location, @map1.mappings[0].location)
! 			assert_kind_of(Bio::Location, @marker2.mappings[0].location)
! 		end
  
!     def test_add_mapping_to_map
! 			@marker1.add_mapping_to_map(@map1, '5')
! 			assert_equal(1, @map1.mappings.length)
! 			assert_equal(1, @marker1.mappings.length)
! 			assert_kind_of(Bio::Location, @map1.mappings[0].location)
! 			assert_kind_of(Bio::Location, @marker1.mappings[0].location)
      end
! 	end
  	
! 	class CloneActsLikeMap
! 		include Bio::Map::ActsLikeMap
! 	end
  	
! 	class TestActsLikeMap < Test::Unit::TestCase
! 		def test_mixin
!       clone = CloneActsLikeMap.new
! 			assert_instance_of(CloneActsLikeMap, clone)
! 			assert_respond_to(clone, 'contains_marker?')
! 			assert_respond_to(clone, 'add_mapping_to_marker')
! 		end
! 	end
! 
! 	class CloneActsLikeMarker
! 		include Bio::Map::ActsLikeMarker
! 	end
  
! 	class TestActsLikeMarker < Test::Unit::TestCase
! 		def test_mixin
! 			clone = CloneActsLikeMarker.new
! 			assert_instance_of(CloneActsLikeMarker, clone)
! 			assert_respond_to(clone, 'mapped_to?')
! 			assert_respond_to(clone, 'add_mapping_to_map')
! 		end
! 	end
  
! 	class CloneActsLikeMapAndMarker
! 		include Bio::Map::ActsLikeMap
! 		include Bio::Map::ActsLikeMarker
! 	end
  
! 	class TestActsLikeMapAndMarker < Test::Unit::TestCase
! 		def test_mixin
! 			clone = CloneActsLikeMapAndMarker.new
! 			assert_instance_of(CloneActsLikeMapAndMarker, clone)
! 			assert_respond_to(clone, 'contains_marker?')
! 			assert_respond_to(clone, 'add_mapping_to_marker')
! 			assert_respond_to(clone, 'mapped_to?')
! 			assert_respond_to(clone, 'add_mapping_to_map')
! 		end
! 	end
  
  end
--- 16,184 ----
  
  module Bio
!   class TestMapSimple < Test::Unit::TestCase
!     def setup
!       @marker1 = Bio::Map::Marker.new('marker1')
!       @marker2 = Bio::Map::Marker.new('marker2')
!       @map1 = Bio::Map::SimpleMap.new('map1', 'some_type', 500, 'some_unit')
!     end
  
!     def test_attributes
!       assert_equal("marker1", @marker1.name)
!       assert_equal("marker2", @marker2.name)
!       assert_equal([], @marker1.mappings_as_marker)
!       assert_equal([], @marker2.mappings_as_marker)
!       assert_equal("map1", @map1.name)
!       assert_equal("some_unit", @map1.units)
!       assert_equal("some_type", @map1.type)
!       assert_equal([], @map1.mappings_as_map)
!     end
!   end
  
!   class TestMapping < Test::Unit::TestCase
!     def setup
!       @marker1 = Bio::Map::Marker.new('marker1')
!       @marker2 = Bio::Map::Marker.new('marker2')
!       @marker3 = Bio::Map::Marker.new('marker3')
!       @map1 = Bio::Map::SimpleMap.new('map1', 'some_type', 'some_unit')
!     end
  
!     def test_add_mapping_as_map
!       @map1.add_mapping_as_map(@marker2, '5')
!       assert_equal(1, @map1.mappings_as_map.length)
!       assert_equal(1, @marker2.mappings_as_marker.length)
!       assert_equal(0, @marker1.mappings_as_marker.length)
!       assert_kind_of(Bio::Locations, @map1.mappings_as_map[0].location)
!       assert_kind_of(Bio::Locations, @marker2.mappings_as_marker[0].location)
!     end
  
!     def test_add_mapping_as_marker
!       @marker1.add_mapping_as_marker(@map1, '5')
!       assert_equal(1, @map1.mappings_as_map.length, 'Mapping as map')
!       assert_equal(1, @marker1.mappings_as_marker.length, 'Mapping as marker')
!       assert_kind_of(Bio::Locations, @map1.mappings_as_map[0].location)
!       assert_kind_of(Bio::Locations, @marker1.mappings_as_marker[0].location)
      end
!     
!     def test_mapped_to?
!       @marker1.add_mapping_as_marker(@map1, '5')
!       assert_equal(true, @marker1.mapped_to?(@map1))
!       assert_equal(false, @marker3.mapped_to?(@map1))
!     end
!     
!     def test_contains_marker?
!       @marker1.add_mapping_as_marker(@map1, '5')
!       assert_equal(true, @map1.contains_marker?(@marker1))
!       assert_equal(false, @map1.contains_marker?(@marker3))
!     end
!     
!     def test_mappings_as_map_each
!       @map1.add_mapping_as_map(@marker1, '5')
!       @marker2.add_mapping_as_marker(@map1, '7')
!       mappings = 0
!       @map1.mappings_as_map.each do |mapping|
!         mappings += 1
!       end
!       assert_equal(2, mappings)
!     end
! 
!     def test_mappings_as_marker_each
!       @map1.add_mapping_as_map(@marker1, '5')
!       @marker1.add_mapping_as_marker(@map1, '7')
!       mappings = 0
!       @marker1.mappings_as_marker.each do |mapping|
!         mappings += 1
!       end
!       assert_equal(2, mappings)
!       
!     end
!     
!     def test_multiple_mappings_between_same_marker_and_map
!       @map1.add_mapping_as_map(@marker1, '5')
!       @map1.add_mapping_as_map(@marker1, '37')
!       @marker1.add_mapping_as_marker(@map1, '53')
!       assert_equal(3, @marker1.mappings_as_marker.length)
! 
!       @marker1.add_mapping_as_marker(@map1, '53')  # This mapping should _not_ be added, because it's already defined.
!       assert_equal(3, @marker1.mappings_as_marker.length)
!     end
!     
!     def test_positions_on
!       @map1.add_mapping_as_map(@marker1, '5')
!       assert_equal(1, @marker1.mappings_as_marker.length)
!       assert_equal('5', @marker1.positions_on(@map1).collect{|p| p.first.from.to_s}.join(',')) # FIXME: Test is not correct (uses Location.first)
!       @map1.add_mapping_as_map(@marker1, '37')
!       assert_equal('5,37', @marker1.positions_on(@map1).collect{|p| p.first.from.to_s}.sort{|a,b| a.to_i <=> b.to_i}.join(',')) # FIXME: Test is not correct (uses Location.first)
!     end
!   end
  	
!   class CloneActsLikeMap
!     include Bio::Map::ActsLikeMap
!     def initialize
!       @mappings_as_map = Array.new
!     end
!     attr_accessor :mappings_as_map
!   end
  	
!   class TestActsLikeMap < Test::Unit::TestCase
!     def setup
!       @clone = CloneActsLikeMap.new
!     end
!     def test_mixin
!       assert_instance_of(CloneActsLikeMap, @clone)
!       assert_respond_to(@clone, 'contains_marker?')
!       assert_respond_to(@clone, 'add_mapping_as_map')
!       assert_equal(0, @clone.mappings_as_map.length)
!     end
!   end
  
!   class CloneActsLikeMarker
!     include Bio::Map::ActsLikeMarker
!     def initialize
!       @mappings_as_marker = Array.new
!     end
!     attr_accessor :mappings_as_marker
!   end
  
!   class TestActsLikeMarker < Test::Unit::TestCase
!     def setup
!       @clone = CloneActsLikeMarker.new
!     end
!     
!     def test_mixin
!       assert_instance_of(CloneActsLikeMarker, @clone)
!       assert_respond_to(@clone, 'mapped_to?')
!       assert_respond_to(@clone, 'add_mapping_as_marker')
!     end
!   end
  
!   class CloneActsLikeMapAndMarker
!     include Bio::Map::ActsLikeMap
!     include Bio::Map::ActsLikeMarker
!     def initialize
!       @mappings_as_map = Array.new
!       @mappings_as_marker = Array.new
!     end
!     attr_accessor :mappings_as_map, :mappings_as_marker
!   end
  
+   class TestActsLikeMapAndMarker < Test::Unit::TestCase
+     def setup
+       @clone_a = CloneActsLikeMapAndMarker.new
+       @clone_b = CloneActsLikeMapAndMarker.new
+       @clone_a.add_mapping_as_map(@clone_b, nil)
+     end
+     
+     def test_mixin
+       assert_instance_of(CloneActsLikeMapAndMarker, @clone_a)
+       assert_respond_to(@clone_a, 'contains_marker?')
+       assert_respond_to(@clone_a, 'add_mapping_as_map')
+       assert_respond_to(@clone_a, 'mapped_to?')
+       assert_respond_to(@clone_a, 'add_mapping_as_marker')
+       
+       assert_equal(1, @clone_a.mappings_as_map.length)
+       assert_equal(0, @clone_a.mappings_as_marker.length)
+       assert_equal(0, @clone_b.mappings_as_map.length)
+       assert_equal(1, @clone_b.mappings_as_marker.length)
+     end
+   end
  end



From ngoto at dev.open-bio.org  Mon Jun 12 10:35:44 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Mon, 12 Jun 2006 10:35:44 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/io flatfile.rb,1.49,1.50
Message-ID: <200606121035.k5CAZiau015926@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/io
In directory dev.open-bio.org:/tmp/cvs-serv15886/lib/bio/io

Modified Files:
	flatfile.rb 
Log Message:
Bio::FlatFile.open(klass, filename) didn't work.


Index: flatfile.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/flatfile.rb,v
retrieving revision 1.49
retrieving revision 1.50
diff -C2 -d -r1.49 -r1.50
*** flatfile.rb	22 Mar 2006 10:19:22 -0000	1.49
--- flatfile.rb	12 Jun 2006 10:35:42 -0000	1.50
***************
*** 426,430 ****
        unless file.respond_to?(:gets)
          # 'file' is a filename
!         self.open_file(file, *arg, &block)
        else
          # 'file' is a IO object
--- 426,430 ----
        unless file.respond_to?(:gets)
          # 'file' is a filename
!         _open_file(dbclass, file, *arg, &block)
        else
          # 'file' is a IO object
***************
*** 466,478 ****
      #
      def self.open_file(filename, *arg)
        if block_given? then
          BufferedInputStream.open_file(filename, *arg) do |stream|
!           yield self.new(nil, stream)
          end
        else
          stream = BufferedInputStream.open_file(filename, *arg)
!         self.new(nil, stream)
        end
      end
  
      # Opens URI specified as _uri_.
--- 466,490 ----
      #
      def self.open_file(filename, *arg)
+       _open_file(nil, filename, *arg)
+     end
+ 
+     # Same as FlatFile.open(dbclass, filename, *arg),
+     # except that it only accept filename and doesn't accept IO object.
+     #
+     # It can accept a block.
+     # If a block is given, it returns the block's return value.
+     # Otherwise, it returns a new FlatFile object.
+     #
+     def self._open_file(dbclass, filename, *arg)
        if block_given? then
          BufferedInputStream.open_file(filename, *arg) do |stream|
!           yield self.new(dbclass, stream)
          end
        else
          stream = BufferedInputStream.open_file(filename, *arg)
!         self.new(dbclass, stream)
        end
      end
+     private_class_method :_open_file
  
      # Opens URI specified as _uri_.



From ngoto at dev.open-bio.org  Thu Jun 15 14:28:57 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Thu, 15 Jun 2006 14:28:57 +0000
Subject: [BioRuby-cvs] bioruby/test/unit/bio/io test_flatfile.rb,NONE,1.1
Message-ID: <200606151428.k5FESvlN028352@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/test/unit/bio/io
In directory dev.open-bio.org:/tmp/cvs-serv28332/test/unit/bio/io

Added Files:
	test_flatfile.rb 
Log Message:
Unit test for Bio::FlatFile class is added but still incomplete.


--- NEW FILE: test_flatfile.rb ---
#
# = test/unit/bio/io/test_flatfile.rb - unit test for Bio::FlatFile
#
#   Copyright (C) 2006 Naohisa Goto <ng at bioruby.org>
#
# License:: Ruby's
#
#  $Id: test_flatfile.rb,v 1.1 2006/06/15 14:28:55 ngoto Exp $
#

require 'pathname'
libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
$:.unshift(libpath) unless $:.include?(libpath)

require 'test/unit'
require 'bio'
require 'stringio'


module Bio
    
module TestFlatFile

  bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4)).cleanpath.to_s
  TestDataPath = Pathname.new(File.join(bioruby_root, 'test', 'data')).cleanpath.to_s
  TestDataFastaFormat01 = File.join(TestDataPath, 'fasta', 'example1.txt')

  class TestBufferedInputStreamClassMethod < Test::Unit::TestCase
    def test_self_for_io
      io = File.open(TestDataFastaFormat01)
      obj = Bio::FlatFile::BufferedInputStream.for_io(io)
      assert_instance_of(Bio::FlatFile::BufferedInputStream, obj)
      assert_equal(TestDataFastaFormat01, obj.path)
    end

    def test_self_open_file
      obj = Bio::FlatFile::BufferedInputStream.open_file(TestDataFastaFormat01)
      assert_instance_of(Bio::FlatFile::BufferedInputStream, obj)
      assert_equal(TestDataFastaFormat01, obj.path)
    end

    def test_self_open_file_with_block
      obj2 = nil
      Bio::FlatFile::BufferedInputStream.open_file(TestDataFastaFormat01) do |obj|
        assert_instance_of(Bio::FlatFile::BufferedInputStream, obj)
        assert_equal(TestDataFastaFormat01, obj.path)
        obj2 = obj
      end
      assert_raise(IOError) { obj2.close }
    end
  end #class TestBufferedInputStreamClassMethod

  class TestBufferedInputStream < Test::Unit::TestCase
    def setup
      io = File.open(TestDataFastaFormat01)
      path = TestDataFastaFormat01
      @obj = Bio::FlatFile::BufferedInputStream.new(io, path)
    end

    def test_to_io
      assert_kind_of(IO, @obj.to_io)
    end

    def test_close
      assert_nil(@obj.close)
    end

    def test_rewind
      @obj.prefetch_gets
      @obj.rewind
      assert_equal('', @obj.prefetch_buffer)
    end

    def test_pos
      @obj.gets
      @obj.gets
      @obj.prefetch_gets
      assert_equal(117, @obj.pos) #the number depends on original data
    end

    def test_pos=()
      str = @obj.gets
      assert_equal(0, @obj.pos = 0)
    end
      
    def test_eof_false_first
      assert_equal(false, @obj.eof?)
    end

    def test_eof_false_after_prefetch
      while @obj.prefetch_gets; nil; end
      assert_equal(false, @obj.eof?)
    end

    def test_eof_true
      while @obj.gets; nil; end
      assert_equal(true, @obj.eof?)
    end

    def test_gets
      @obj.gets
      @obj.gets
      assert_equal("gagcaaatcgaaaaggagagatttctgcatatcaagagaaaattcgagctgagatacattccaagtgtggctactc", @obj.gets.chomp)
    end

    def test_gets_equal_prefetch_gets
      @obj.prefetch_gets
      str = @obj.prefetch_gets
      @obj.prefetch_gets
      @obj.gets
      assert_equal(@obj.gets, str)
    end

    def test_ungets
      @obj.gets
      @obj.gets
      str1 = @obj.gets
      str2 = @obj.gets
      assert_nil(@obj.ungets(str2))
      assert_nil(@obj.ungets(str1))
      assert_equal(str1, @obj.gets)
      assert_equal(str2, @obj.gets)
    end

    def test_getc
      assert_equal(?>, @obj.getc)
    end

    def test_getc_after_prefetch
      @obj.prefetch_gets
      assert_equal(?>, @obj.getc)
    end

    def test_ungetc
      c = @obj.getc
      assert_nil(@obj.ungetc(c))
      assert_equal(c, @obj.getc)
    end

    def test_ungetc_after_prefetch
      str = @obj.prefetch_gets
      c = @obj.getc
      assert_nil(@obj.ungetc(c))
      assert_equal(str, @obj.gets)
    end

    def test_prefetch_buffer
      str = @obj.prefetch_gets
      str += @obj.prefetch_gets
      assert_equal(str, @obj.prefetch_buffer)
    end

    def test_prefetch_gets
      @obj.prefetch_gets
      @obj.prefetch_gets
      @obj.gets
      str = @obj.prefetch_gets
      @obj.gets
      assert_equal(str, @obj.gets)
    end

    def test_prefetch_gets_with_arg
      # test @obj.gets
      str = @obj.prefetch_gets("\n>")
      assert_equal(str, @obj.gets("\n>"))
      # test using IO object
      io = @obj.to_io
      io.rewind
      assert_equal(str, io.gets("\n>"))
    end

    def test_skip_spaces
      @obj.gets('CDS')
      assert_nil(@obj.skip_spaces)
      assert_equal(?a, @obj.getc)
    end
                   
  end #class TestBufferedInputStream

  class TestFlatFileWithCustomClass < Test::Unit::TestCase

    # very simple parser for tab-separated data
    class SimpleFormat
      # delimiter needed for flatfile
      DELIMITER = RS = nil # nil means no delimiter and reading entire file
      def initialize(str)
        @data = str.split(/\n/).collect { |x| x.to_s.split(/\t/) }
      end
      attr_reader :data
    end

    def test_simpleformat
      testdata = "AAA\tBBB\tCCCCC\tDDDD\n123\t456\n"
      testio = StringIO.new(testdata)
      Bio::FlatFile.open(SimpleFormat, testio) do |ff|
        ff.each do |entry|
          assert_equal([ [ 'AAA', 'BBB', 'CCCCC', 'DDDD' ],
                         [ '123', '456' ] ], entry.data)
        end
      end
    end

    # very simple parser for "//"-separated entries
    class SimpleFormat2
      # delimiter needed for flatfile
      DELIMITER = RS = "//\n" # the end of each entry is "//\n"
      def initialize(str)
        # very simple parser only to store a text data
        @data = str
      end
      attr_reader :data
    end

    def test_simpleformat2
      testdata = <<__END_OF_TESTDATA__
test01
This is a test.
//
test02
This is an example.
//
__END_OF_TESTDATA__
      a = testdata.split(/(\/\/\n)/)
      results = [ a[0]+a[1], a[2]+a[3] ]
      testio = StringIO.new(testdata)
      Bio::FlatFile.open(SimpleFormat2, testio) do |ff|
        ff.each do |entry|
          assert_equal(results.shift, entry.data)
        end
      end
    end

  end #class TestFlatFileWithCustomClass

end #module TestFlatFile

end #module Bio



From nakao at dev.open-bio.org  Fri Jun 16 16:51:07 2006
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Fri, 16 Jun 2006 16:51:07 +0000
Subject: [BioRuby-cvs] bioruby/test/unit/bio/db/embl test_sptr.rb,1.2,1.3
Message-ID: <200606161651.k5GGp7aH001256@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/test/unit/bio/db/embl
In directory dev.open-bio.org:/tmp/cvs-serv1236

Modified Files:
	test_sptr.rb 
Log Message:
* Added a test in test_ft.


Index: test_sptr.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/db/embl/test_sptr.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** test_sptr.rb	23 Nov 2005 10:06:12 -0000	1.2
--- test_sptr.rb	16 Jun 2006 16:51:05 -0000	1.3
***************
*** 234,238 ****
        assert(@obj.ft)
        name = 'DNA_BIND'
!       assert_equal([{"FTId"=>nil, "From"=>102, "diff"=>[], "To"=>292, "Description"=>nil}], @obj.ft(name))
      end
  
--- 234,239 ----
        assert(@obj.ft)
        name = 'DNA_BIND'
!       assert_equal([{"FTId"=>"", "From"=>102, "diff"=>[], "To"=>292, "Description"=>""}], @obj.ft(name))
!       assert_equal([{"FTId"=>"", "From"=>102, "diff"=>[], "To"=>292, "Description"=>""}], @obj.ft[name])
      end
  



From nakao at dev.open-bio.org  Fri Jun 16 17:01:03 2006
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Fri, 16 Jun 2006 17:01:03 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/db/embl sptr.rb,1.31,1.32
Message-ID: <200606161701.k5GH13j4001328@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/db/embl
In directory dev.open-bio.org:/tmp/cvs-serv1306

Modified Files:
	sptr.rb 
Log Message:
* fixed a PROPEP parsing bug in Bio::SPTR#ft. (reported by Makoto 
  Hamaguchi-san).
* changed codes in the Bio::SPTR#id_line and the Bio::SPTR#dt. [refactoring] 


Index: sptr.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/embl/sptr.rb,v
retrieving revision 1.31
retrieving revision 1.32
diff -C2 -d -r1.31 -r1.32
*** sptr.rb	14 Apr 2006 05:52:28 -0000	1.31
--- sptr.rb	16 Jun 2006 17:01:01 -0000	1.32
***************
*** 2,6 ****
  # = bio/db/embl/sptr.rb - UniProt/SwissProt and TrEMBL database class
  # 
! # Copyright::   Copyright (C) 2001-2006 Mitsuteru C. Nakao <n at bioruby.org>
  # License::     Ruby's
  #
--- 2,6 ----
  # = bio/db/embl/sptr.rb - UniProt/SwissProt and TrEMBL database class
  # 
! # Copyright::   Copyright (C) 2001-2006  Mitsuteru C. Nakao <n at bioruby.org>
  # License::     Ruby's
  #
***************
*** 46,50 ****
    @@data_class = ["STANDARD", "PRELIMINARY"]
  
-   
    # returns a Hash of the ID line.
    #
--- 46,49 ----
***************
*** 57,84 ****
    #
    # === Examples
!   #   obj.id_line  #=> {"ENTRY_NAME"=>"P53_HUMAN", "DATA_CLASS"=>"STANDARD", "SEQUENCE_LENGTH"=>393, "MOLECULE_TYPE"=>"PRT"}
    #
    #   obj.id_line('ENTRY_NAME') #=> "P53_HUMAN"
    #
    def id_line(key = nil)
!     unless @data['ID']
!       tmp = Hash.new
!       a = @orig['ID'].split(/ +/)         
!       tmp['ENTRY_NAME']      = a[1]
!       tmp['DATA_CLASS']      = a[2].sub(/;/,'') 
!       tmp['MOLECULE_TYPE']   = a[3].sub(/;/,'')
!       tmp['SEQUENCE_LENGTH'] = a[4].to_i
!       @data['ID'] = tmp
!     end
  
!     if key
!       @data['ID'][key] # String/Int
!     else
!       @data['ID']      # Hash
!     end
    end
  
  
- 
    # returns a ENTRY_NAME in the ID line. 
    #
--- 56,78 ----
    #
    # === Examples
!   #   obj.id_line  #=> {"ENTRY_NAME"=>"P53_HUMAN", "DATA_CLASS"=>"STANDARD", 
!   #                     "SEQUENCE_LENGTH"=>393, "MOLECULE_TYPE"=>"PRT"}
    #
    #   obj.id_line('ENTRY_NAME') #=> "P53_HUMAN"
    #
    def id_line(key = nil)
!     return id_line[key] if key
!     return @data['ID'] if @data['ID']
  
!     part = @orig['ID'].split(/ +/)         
!     @data['ID'] = {
!       'ENTRY_NAME'      => part[1],
!       'DATA_CLASS'      => part[2].sub(/;/,''),
!       'MOLECULE_TYPE'   => part[3].sub(/;/,''),
!       'SEQUENCE_LENGTH' => part[4].to_i 
!     }
    end
  
  
    # returns a ENTRY_NAME in the ID line. 
    #
***************
*** 128,145 ****
    #   DT DD-MMM-YYY (rel. NN, Last annotation update)
    def dt(key = nil)
!     unless @data['DT']
!       tmp = Hash.new
!       a = self.get('DT').split(/\n/)
!       tmp['created']    = a[0].sub(/\w{2}   /,'').strip
!       tmp['sequence']   = a[1].sub(/\w{2}   /,'').strip
!       tmp['annotation'] = a[2].sub(/\w{2}   /,'').strip
!       @data['DT'] = tmp
!     end
  
!     if key
!       @data['DT'][key]
!     else
!       @data['DT']
!     end
    end
  
--- 122,134 ----
    #   DT DD-MMM-YYY (rel. NN, Last annotation update)
    def dt(key = nil)
!     return dt[key] if key
!     return @data['DT'] if @data['DT']
  
!     part = self.get('DT').split(/\n/)
!     @data['DT'] = {
!       'created'    => part[0].sub(/\w{2}   /,'').strip,
!       'sequence'   => part[1].sub(/\w{2}   /,'').strip,
!       'annotation' => part[2].sub(/\w{2}   /,'').strip
!     }
    end
  
***************
*** 451,455 ****
  
        # Event, Named isoforms, Comment, [Name, Synonyms, IsoId, Sequnce]+
!       tmp = {'Event' => nil, 'Named isoforms' => nil, 'Comment' => nil, 'Variants'  => []}
  
        if /Event=(.+?);/ =~ ap
--- 440,445 ----
  
        # Event, Named isoforms, Comment, [Name, Synonyms, IsoId, Sequnce]+
!       tmp = {'Event' => nil, 'Named isoforms' => nil, 'Comment' => nil, 
!              'Variants'  => []}
  
        if /Event=(.+?);/ =~ ap
***************
*** 499,503 ****
  
        ms.each do |m|
!         mass = {'MW'=>nil,'MW_ERR'=>nil,'METHOD'=>nil,'RANGE'=>nil}
          m.sub(/.$/,'').split(/;/).each do |line|
            case line
--- 489,493 ----
  
        ms.each do |m|
!         mass = {'MW' => nil,'MW_ERR' => nil,'METHOD' => nil,'RANGE' => nil}
          m.sub(/.$/,'').split(/;/).each do |line|
            case line
***************
*** 550,554 ****
      it.map {|ent|
        {:partner_id => ent[0].strip,
!        :nbexp => ent[1].strip, 
         :intact_acc => ent[2].split(', ') }
      }
--- 540,544 ----
      it.map {|ent|
        {:partner_id => ent[0].strip,
!        :nbexp      => ent[1].strip, 
         :intact_acc => ent[2].split(', ') }
      }
***************
*** 577,583 ****
  
    # returns conteins in the feature table.
    # * Bio::SPTR#ft -> Hash
!   #    {'feature_name' => [{'From' => str, 'To' => str,
!   #                         'Description' => str, 'FTId' => str}],...}
    #
    # returns an Array of the information about the feature_name in the feature table.
--- 567,589 ----
  
    # returns conteins in the feature table.
+   #
+   # == Examples
+   #
+   #  sp = Bio::SPTR.new(entry)
+   #  ft = sp.ft
+   #  ft.class #=> Hash
+   #  ft.keys.each do |feature_key|
+   #    ft[feature_key].each do |feature|
+   #      feature['From'] #=> '1'
+   #      feature['To']   #=> '21'
+   #      feature['Description'] #=> ''
+   #      feature['FTId'] #=> ''
+   #      feature['diff'] #=> []
+   #    end
+   #  end
+   #
    # * Bio::SPTR#ft -> Hash
!   #    {FEATURE_KEY => [{'From' => int, 'To' => int, 'diff' => [],
!   #                      'Description' => aStr, 'FTId' => aStr}],...}
    #
    # returns an Array of the information about the feature_name in the feature table.
***************
*** 595,692 ****
    #   35-75   Description (>=0 per key)
    #   -----   -----------------
!   def ft(feature_name = nil)
!     unless @data['FT']
!       table        = Hash.new()
!       last_feature = nil
! 
!       begin
!         get('FT').split(/\n/).each {|line|
! 
!           feature = line[5..12].strip
! 
!           if feature == '' and line[34..74]
!             tmp = ' ' + line[34..74].strip 
!             table[last_feature].last['Description'] << tmp
!             
!             next unless /\.$/ =~ line
!           else
!             from = line[14..19].strip
!             to   = line[21..26].strip
!             desc = line[34..74].strip if line[34..74]
  
!             table[feature] = [] unless table[feature]
!             table[feature] << {
!               'From'        => from.to_i, 
!               'To'          => to.to_i, 
!               'Description' => desc,
!               'diff'        => [],
!               'FTId'        => nil }
!             last_feature = feature
!             next
!           end
  
!           case last_feature
!           when 'VARSPLIC', 'VARIANT', 'CONFLICT'
!             if /FTId=(.+?)\./ =~ line   # version 41 >
!               ftid = $1
!               table[last_feature].last['FTId'] = ftid
!               table[last_feature].last['Description'].sub!(/ \/FTId=#{ftid}./,'') 
!             end
  
!             case table[last_feature].last['Description']
!             when /(\w[\w ]*\w*) - ?> (\w[\w ]*\w*)/
!               original = $1
!               swap = $2
!               original = original.gsub(/ /,'').strip
!               swap = swap.gsub(/ /,'').strip
!             when /Missing/i
!               original = seq.subseq(table[last_feature].last['From'],
!                                     table[last_feature].last['To'])
!               swap = ''
!             else
!               raise line
!             end
!             table[last_feature].last['diff'] = [original, swap]
!           end
!         }
  
!       rescue
!         raise "Invalid FT Lines(#{$!}) in #{entry_id}:, \n" + 
!                   "'#{self.get('FT')}'\n"
!       end
  
!       table.each_key do |k|
!         table[k].each do |e|
!           if / -> / =~ e['Description']
!             pattern = /([A-Z][A-Z ]*[A-Z]*) -> ([A-Z][A-Z ]*[A-Z]*)/
!             e['Description'].sub!(pattern) {  
!               a = $1
!               b = $2
!               a.gsub(/ /,'') + " -> " + b.gsub(/ /,'') 
!             }
!           end
!           if /- [\w\d]/ =~ e['Description']
!             e['Description'].gsub!(/([\w\d]- [\w\d]+)/) { 
!               a = $1
!               if /- AND/ =~ a
!                 a
!               else
!                 a.sub(/ /,'') 
!               end
!             }
!           end
          end
        end
-       @data['FT'] = table
      end
! 
!     if feature_name
!       @data['FT'][feature_name]
!     else
!       @data['FT']
      end
    end
  
  
    # returns a Hash of conteins in the SQ lines.
    # * Bio::SPTRL#sq  -> hsh
--- 601,670 ----
    #   35-75   Description (>=0 per key)
    #   -----   -----------------
!   #
!   def ft(feature_key = nil)
!     return ft[feature_key] if feature_key
!     return @data['FT'] if @data['FT']
  
!     table = []
!     begin
!     get('FT').split("\n").each do |line|
!       if line =~ /^FT   \w/
!         feature = line.chomp.ljust(74)
!         table << [feature[ 5..12].strip,   # Feature Name
!                   feature[14..19].strip,   # From
!                   feature[21..26].strip,   # To
!                   feature[34..74].strip ]  # Description
!       else
!         table.last << line.chomp.sub!(/^FT +/, '')
!       end
!     end
  
!     # Join Desctiption lines
!     table = table.map { |feature| 
!       ftid = feature.pop if feature.last =~ /FTId=/
!       if feature.size > 4
!         feature = [feature[0], feature[1], feature[2], 
!                    feature[3, feature.size - 3].join(" ")]
!       end
!       feature << ftid
!     }
  
!     hash = {}
!     table.each do |feature|
!       hash[feature[0]] = [] unless hash[feature[0]]
  
!       hash[feature[0]] << {
!         'From' => feature[1].to_i, 
!         'To'   => feature[2].to_i, 
!         'Description' => feature[3], 
!         'FTId' => feature[4].to_s.sub(/\/FTId=/, '').sub(/\.$/, ''),
!         'diff' => []
!       }
  
!       case feature[0]
!       when 'VARSPLIC', 'VARIANT', 'VAR_SEQ', 'CONFLICT'
!         case hash[feature[0]].last['Description']
!         when /(\w[\w ]*\w*) - ?> (\w[\w ]*\w*)/
!           original_res = $1
!           changed_res = $2
!           original_res = original_res.gsub(/ /,'').strip
!           chenged_res = changed_res.gsub(/ /,'').strip
!         when /Missing/i
!           original_res = seq.subseq(hash[feature[0]].last['From'],
!                                     hash[feature[0]].last['To'])
!           changed_res = ''
          end
+         hash[feature[0]].last['diff'] = [original_res, chenged_res]
        end
      end
!     rescue
!       raise "Invalid FT Lines(#{$!}) in #{entry_id}:, \n'#{self.get('FT')}'\n"
      end
+ 
+     @data['FT'] = hash
    end
  
  
+ 
    # returns a Hash of conteins in the SQ lines.
    # * Bio::SPTRL#sq  -> hsh
***************
*** 694,698 ****
    # returns a value of a key given in the SQ lines.
    # * Bio::SPTRL#sq(key)  -> int or str
!   # * Keys: ['MW', 'mw', 'molecular', 'weight', 'aalen', 'len', 'length', 'CRC64']
    #
    # === SQ Line; sequence header (1/entry)
--- 672,677 ----
    # returns a value of a key given in the SQ lines.
    # * Bio::SPTRL#sq(key)  -> int or str
!   # * Keys: ['MW', 'mw', 'molecular', 'weight', 'aalen', 'len', 'length', 
!   #          'CRC64']
    #
    # === SQ Line; sequence header (1/entry)



From ngoto at dev.open-bio.org  Tue Jun 20 14:21:37 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Tue, 20 Jun 2006 14:21:37 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/blat report.rb,1.7,1.8
Message-ID: <200606201421.k5KELbnB001117@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl/blat
In directory dev.open-bio.org:/tmp/cvs-serv1058

Modified Files:
	report.rb 
Log Message:
Added Bio::BLAT::Report::Hit#milli_bad, #percent_identity, #protein?,
and #score methods. The algorithm of these methods are described in
the BLAT FAQ (http://genome.ucsc.edu/FAQ/FAQblat#blat5).
Thanks to Dr. Itoshi Nikaido for help.


Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blat/report.rb,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** report.rb	8 May 2006 14:37:55 -0000	1.7
--- report.rb	20 Jun 2006 14:21:34 -0000	1.8
***************
*** 328,331 ****
--- 328,405 ----
            exons.each(&x)
          end
+ 
+         #--
+         # methods described in the BLAT FAQ at the UCSC genome browser.
+         # (http://genome.ucsc.edu/FAQ/FAQblat#blat5)
+         #++
+ 
+         # Calculates the pslCalcMilliBad value defined in the
+         # BLAT FAQ (http://genome.ucsc.edu/FAQ/FAQblat#blat5).
+         #
+         # The algorithm is taken from the BLAT FAQ
+         # (http://genome.ucsc.edu/FAQ/FAQblat#blat5).
+         def milli_bad
+           w = (self.protein? ? 3 : 1)
+           qalen = w * (self.query.end - self.query.start)
+           talen = self.target.end - self.target.start
+           alen = (if qalen < talen then qalen; else talen; end)
+           return 0 if alen <= 0
+           d = qalen - talen
+           d = 0 if d < 0
+           total = w * (self.match + self.rep_match + self.mismatch)
+           return 0 if total == 0
+           return (1000 * (self.mismatch * w + self.query.gap_count +
+                             (3 * Math.log(1 + d)).round) / total)
+         end
+ 
+         # Calculates the percent identity compatible with the BLAT web server
+         # as described in the BLAT FAQ
+         # (http://genome.ucsc.edu/FAQ/FAQblat#blat5).
+         #
+         # The algorithm is taken from the BLAT FAQ
+         # (http://genome.ucsc.edu/FAQ/FAQblat#blat5).
+         def percent_identity
+           100.0 - self.milli_bad * 0.1
+         end
+ 
+         # When the output data comes from the protein query, returns true.
+         # Otherwise (nucleotide query), returns false.
+         # It returns nil if this cannot be determined.
+         #
+         # The algorithm is taken from the BLAT FAQ
+         # (http://genome.ucsc.edu/FAQ/FAQblat#blat5).
+         def protein?
+           return nil if self.block_sizes.empty?
+           case self.strand
+           when '+'
+             if self.target.end == self.target.starts[-1] +
+                 3 * self.block_sizes[-1] then
+               true
+             else
+               false
+             end
+           when '-'
+             if self.target.start == self.target.size -
+                 self.target.starts[-1] + 3 * self.block_sizes[-1] then
+               true
+             else
+               false
+             end
+           else
+             nil
+           end
+         end
+ 
+         # Calculates the score compatible with the BLAT web server
+         # as described in the BLAT FAQ
+         # (http://genome.ucsc.edu/FAQ/FAQblat#blat5).
+         #
+         # The algorithm is taken from the BLAT FAQ
+         # (http://genome.ucsc.edu/FAQ/FAQblat#blat5).
+         def score
+           w = (self.protein? ? 3 : 1)
+           w * (self.match + (self.rep_match >> 1)) -
+             w * self.mismatch - self.query.gap_count - self.target.gap_count
+         end
        end #class Hit
  



From ngoto at dev.open-bio.org  Tue Jun 20 14:34:40 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Tue, 20 Jun 2006 14:34:40 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/blat report.rb,1.8,1.9
Message-ID: <200606201434.k5KEYeDQ001282@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl/blat
In directory dev.open-bio.org:/tmp/cvs-serv1262

Modified Files:
	report.rb 
Log Message:
Changed some documents.
Reference: http://genome.ucsc.edu/goldenPath/help/blatSpec.html


Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blat/report.rb,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** report.rb	20 Jun 2006 14:21:34 -0000	1.8
--- report.rb	20 Jun 2006 14:34:38 -0000	1.9
***************
*** 21,25 ****
  #   Genome Research, 12, 656--664, 2002.
  #   http://www.genome.org/cgi/content/abstract/12/4/656
! # 
  
  require 'bio'
--- 21,25 ----
  #   Genome Research, 12, 656--664, 2002.
  #   http://www.genome.org/cgi/content/abstract/12/4/656
! # * http://genome.ucsc.edu/goldenPath/help/blatSpec.html
  
  require 'bio'
***************
*** 262,268 ****
          # Mismatch nucleotides.
          def mismatch;    @data[1].to_i;  end
!         # rep. match (???)
          def rep_match;   @data[2].to_i;  end
!         # N's (???)
          def n_s;         @data[3].to_i;  end
  
--- 262,272 ----
          # Mismatch nucleotides.
          def mismatch;    @data[1].to_i;  end
! 
!         # "rep. match".
!         # Number of bases that match but are part of repeats.
!         # Note that current version of BLAT always set 0.
          def rep_match;   @data[2].to_i;  end
! 
!         # "N's". Number of 'N' bases.
          def n_s;         @data[3].to_i;  end
  



From ngoto at dev.open-bio.org  Thu Jun 22 14:32:49 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Thu, 22 Jun 2006 14:32:49 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/io flatfile.rb,1.50,1.51
Message-ID: <200606221432.k5MEWnV4007918@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/io
In directory dev.open-bio.org:/tmp/cvs-serv7898/lib/bio/io

Modified Files:
	flatfile.rb 
Log Message:
Fixed: failed to autodetect psLayout version 4 (Bio::BLAT::Report)


Index: flatfile.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/flatfile.rb,v
retrieving revision 1.50
retrieving revision 1.51
diff -C2 -d -r1.50 -r1.51
*** flatfile.rb	12 Jun 2006 10:35:42 -0000	1.50
--- flatfile.rb	22 Jun 2006 14:32:47 -0000	1.51
***************
*** 1196,1200 ****
  
            blat   = RuleRegexp[ 'Bio::Blat::Report',
!             /^psLayout version \d+\s*$/ ],
            spidey = RuleRegexp[ 'Bio::Spidey::Report',
              /^\-\-SPIDEY version .+\-\-$/ ],
--- 1196,1200 ----
  
            blat   = RuleRegexp[ 'Bio::Blat::Report',
!             /^psLayout version \d+/ ],
            spidey = RuleRegexp[ 'Bio::Spidey::Report',
              /^\-\-SPIDEY version .+\-\-$/ ],



From ngoto at dev.open-bio.org  Tue Jun 27 05:44:59 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Tue, 27 Jun 2006 05:44:59 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/sequence na.rb,1.3,1.4
Message-ID: <200606270544.k5R5ixTu007673@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/sequence
In directory dev.open-bio.org:/tmp/cvs-serv7649/lib/bio/sequence

Modified Files:
	na.rb 
Log Message:
Bio::Sequence::NA#gc_content, #at_content, #gc_skew, #at_skew
are newly added.
Bio::Sequence::NA#gc_percent are changed not to raise ZeroDivisionError
and returns 0 when given sequence is empty.


Index: na.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence/na.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** na.rb	26 Mar 2006 02:27:59 -0000	1.3
--- na.rb	27 Jun 2006 05:44:57 -0000	1.4
***************
*** 282,286 ****
  
    # Calculate the ratio of GC / ATGC bases as a percentage rounded to 
!   # the nearest whole number.
    #
    #   s = Bio::Sequence::NA.new('atggcgtga')
--- 282,286 ----
  
    # Calculate the ratio of GC / ATGC bases as a percentage rounded to 
!   # the nearest whole number. U is regarded as T.
    #
    #   s = Bio::Sequence::NA.new('atggcgtga')
***************
*** 292,299 ****
--- 292,356 ----
      at = count['a'] + count['t'] + count['u']
      gc = count['g'] + count['c']
+     return 0 if at + gc == 0
      gc = 100 * gc / (at + gc)
      return gc
    end
  
+   # Calculate the ratio of GC / ATGC bases. U is regarded as T.
+   #
+   #   s = Bio::Sequence::NA.new('atggcgtga')
+   #   puts s.gc_content                       #=> 0.555555555555556
+   # ---
+   # *Returns*:: Float
+   def gc_content
+     count = self.composition
+     at = count['a'] + count['t'] + count['u']
+     gc = count['g'] + count['c']
+     return 0.0 if at + gc == 0
+     return (gc.to_f / (at + gc).to_f)
+   end
+ 
+   # Calculate the ratio of AT / ATGC bases. U is regarded as T.
+   #
+   #   s = Bio::Sequence::NA.new('atggcgtga')
+   #   puts s.at_content                       #=> 0.444444444444444
+   # ---
+   # *Returns*:: Float
+   def at_content
+     count = self.composition
+     at = count['a'] + count['t'] + count['u']
+     gc = count['g'] + count['c']
+     return 0.0 if at + gc == 0
+     return (at.to_f / (at + gc).to_f)
+   end
+ 
+   # Calculate the ratio of (G - C) / (G + C) bases.
+   #
+   #   s = Bio::Sequence::NA.new('atggcgtga')
+   #   puts s.gc_skew                          #=> 0.6
+   # ---
+   # *Returns*:: Float
+   def gc_skew
+     count = self.composition
+     g = count['g']
+     c = count['c']
+     return 0.0 if g + c == 0
+     return ((g - c).to_f / (g + c).to_f)
+   end
+ 
+   # Calculate the ratio of (A - T) / (A + T) bases. U is regarded as T.
+   #
+   #   s = Bio::Sequence::NA.new('atgttgttgttc')
+   #   puts s.at_skew                          #=> -0.75
+   # ---
+   # *Returns*:: Float
+   def at_skew
+     count = self.composition
+     a = count['a']
+     t = count['t'] + count['u']
+     return 0.0 if a + t == 0
+     return ((a - t).to_f / (a + t).to_f)
+   end
+ 
    # Returns an alphabetically sorted array of any non-standard bases 
    # (other than 'atgcu').



From ngoto at dev.open-bio.org  Tue Jun 27 05:44:59 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Tue, 27 Jun 2006 05:44:59 +0000
Subject: [BioRuby-cvs] bioruby/test/unit/bio/sequence test_na.rb,1.1,1.2
Message-ID: <200606270544.k5R5ixYo007678@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/test/unit/bio/sequence
In directory dev.open-bio.org:/tmp/cvs-serv7649/test/unit/bio/sequence

Modified Files:
	test_na.rb 
Log Message:
Bio::Sequence::NA#gc_content, #at_content, #gc_skew, #at_skew
are newly added.
Bio::Sequence::NA#gc_percent are changed not to raise ZeroDivisionError
and returns 0 when given sequence is empty.


Index: test_na.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/sequence/test_na.rb,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** test_na.rb	8 Feb 2006 07:08:22 -0000	1.1
--- test_na.rb	27 Jun 2006 05:44:57 -0000	1.2
***************
*** 99,102 ****
--- 99,128 ----
      end
  
+     def test_gc_content
+       assert_in_delta(0.4, @obj.gc_content, Float::EPSILON)
+       @obj[0, 1] = 'g'
+       assert_in_delta(0.45, @obj.gc_content, Float::EPSILON)
+     end
+ 
+     def test_at_content
+       assert_in_delta(0.6, @obj.at_content, Float::EPSILON)
+       @obj[0, 1] = 'g'
+       assert_in_delta(0.55, @obj.at_content, Float::EPSILON)
+     end
+ 
+     def test_gc_skew
+       assert_in_delta(0.0, @obj.gc_skew, Float::EPSILON)
+       @obj[0, 1] = 'g'
+       assert_in_delta(1.0/9.0, @obj.gc_skew, Float::EPSILON)
+       @obj.gsub!(/a/, 'c')
+       assert_in_delta(-3.0/8.0, @obj.gc_skew, Float::EPSILON)
+     end
+ 
+     def test_at_skew
+       assert_in_delta(1.0/3.0, @obj.at_skew, Float::EPSILON)
+       @obj[0, 1] = 'g'
+       assert_in_delta(3.0/11.0, @obj.at_skew, Float::EPSILON)
+     end
+ 
      def test_iliegal_bases
        @obj[0, 1] = 'n'



From ngoto at dev.open-bio.org  Tue Jun 27 05:44:59 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Tue, 27 Jun 2006 05:44:59 +0000
Subject: [BioRuby-cvs] bioruby ChangeLog,1.52,1.53
Message-ID: <200606270544.k5R5ixDT007683@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby
In directory dev.open-bio.org:/tmp/cvs-serv7649

Modified Files:
	ChangeLog 
Log Message:
Bio::Sequence::NA#gc_content, #at_content, #gc_skew, #at_skew
are newly added.
Bio::Sequence::NA#gc_percent are changed not to raise ZeroDivisionError
and returns 0 when given sequence is empty.


Index: ChangeLog
===================================================================
RCS file: /home/repository/bioruby/bioruby/ChangeLog,v
retrieving revision 1.52
retrieving revision 1.53
diff -C2 -d -r1.52 -r1.53
*** ChangeLog	3 May 2006 00:07:58 -0000	1.52
--- ChangeLog	27 Jun 2006 05:44:57 -0000	1.53
***************
*** 1,2 ****
--- 1,11 ----
+ 2006-06-27  Naohisa Goto <ng at bioruby.org>
+ 
+         * lib/bio/sequence/na.rb
+ 
+           Bio::Sequence::NA#gc_content, #at_content, #gc_skew, #at_skew
+ 	  are newly added. Bio::Sequence::NA#gc_percent are changed
+ 	  not to raise ZeroDivisionError and returns 0 when given sequence
+ 	  is empty.
+ 
  2006-05-02  Mitsuteru Nakao <n at bioruby.org>
  



From aerts at dev.open-bio.org  Tue Jun 27 12:37:44 2006
From: aerts at dev.open-bio.org (Jan Aerts)
Date: Tue, 27 Jun 2006 12:37:44 +0000
Subject: [BioRuby-cvs] bioruby/test/unit/bio test_map.rb,1.2,1.3
Message-ID: <200606271237.k5RCbimc008730@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/test/unit/bio
In directory dev.open-bio.org:/tmp/cvs-serv8703/test/unit/bio

Modified Files:
	test_map.rb 
Log Message:
Removed Enumerable mixin from ActsLikeMap and ActsLikeMarker, because 'def each' would be ambiguous.
Included examples for using ActsLikeMap and ActsLikeMarker.


Index: test_map.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/test_map.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** test_map.rb	7 Jun 2006 12:56:29 -0000	1.2
--- test_map.rb	27 Jun 2006 12:37:42 -0000	1.3
***************
*** 6,10 ****
  # License::     Ruby's
  #
! # $Id$
  
  require 'pathname'
--- 6,10 ----
  # License::     Ruby's
  #
! # $Id:
  
  require 'pathname'
***************
*** 182,184 ****
--- 182,197 ----
      end
    end
+   
+   class Clone
+     include Bio::Map::ActsLikeMap
+     include Bio::Map::ActsLikeMarker
+     
+     def initialize(name)
+       @name = name
+       @mappings_as_map = Array.new
+       @mappings_as_marker = Array.new
+     end
+     attr_accessor :name, :mappings_as_map, :mappings_as_marker
+   end
+   
  end



From aerts at dev.open-bio.org  Tue Jun 27 12:37:44 2006
From: aerts at dev.open-bio.org (Jan Aerts)
Date: Tue, 27 Jun 2006 12:37:44 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio map.rb,1.6,1.7
Message-ID: <200606271237.k5RCbiae008725@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv8703/lib/bio

Modified Files:
	map.rb 
Log Message:
Removed Enumerable mixin from ActsLikeMap and ActsLikeMarker, because 'def each' would be ambiguous.
Included examples for using ActsLikeMap and ActsLikeMarker.


Index: map.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/map.rb,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** map.rb	7 Jun 2006 12:55:50 -0000	1.6
--- map.rb	27 Jun 2006 12:37:42 -0000	1.7
***************
*** 6,10 ****
  # Licence::     Ruby's
  #
! # $Id$
  require 'bio/location'
  
--- 6,10 ----
  # Licence::     Ruby's
  #
! # $Id:
  require 'bio/location'
  
***************
*** 65,74 ****
    #  puts "Does my_map2 contain marker3? => " + my_map2.contains_marker?(my_marker3).to_s
    #  
!   #  my_map1.sort.each do |mapping|
!   #    puts mapping.map.name + "\t" + mapping.marker.name + "\t" + mapping.location[0].from.to_s + ".." + mapping.location[-1].to.to_s
    #  end
!   #  puts my_map1.min.marker.name
!   #  my_map2.each do |mapping|
!   #    puts mapping.map.name + "\t" + mapping.marker.name + "\t" + mapping.location[0].from.to_s + ".." + mapping.location[-1].to.to_s
    #  end
    module Map
--- 65,74 ----
    #  puts "Does my_map2 contain marker3? => " + my_map2.contains_marker?(my_marker3).to_s
    #  
!   #  my_map1.mappings_as_map.sort.each do |mapping|
!   #    puts mapping.map.name + "\t" + mapping.marker.name + "\t" + mapping.location.from.to_s + ".." + mapping.location.to.to_s
    #  end
!   #  puts my_map1.mappings_as_map.min.marker.name
!   #  my_map2.mappings_as_map.each do |mapping|
!   #    puts mapping.map.name + "\t" + mapping.marker.name + "\t" + mapping.location.from.to_s + ".." + mapping.location.to.to_s
    #  end
    module Map
***************
*** 81,84 ****
--- 81,94 ----
    # 
    # Classes that include this mixin should provide an array property called mappings_as_map.
+   # For example:
+   #   class MyMapThing
+   #     include Bio::Map::ActsLikeMap
+   #     
+   #     def initialize (name)
+   #       @name = name
+   #       @mappings_as_maps = Array.new
+   #     end
+   #     attr_accessor :name, :mappings_as_map
+   #    end
      module ActsLikeMap
        include Enumerable
***************
*** 138,147 ****
        end
        
-       # Go through all Bio::Map::Mapping objects linked to this Bio::Map::SimpleMap.
-       def each
-         self.mappings_as_map.each do |mapping|
-           yield mapping
-         end
-       end
      end #ActsLikeMap
  
--- 148,151 ----
***************
*** 154,157 ****
--- 158,171 ----
      # 
      # Classes that include this mixin should provide an array property called mappings_as_marker.
+     # For example:
+     #   class MyMarkerThing
+     #     include Bio::Map::ActsLikeMarker
+     #     
+     #     def initialize (name)
+     #       @name = name
+     #       @mappings_as_marker = Array.new
+     #     end
+     #     attr_accessor :name, :mappings_as_marker
+     #    end
      module ActsLikeMarker
        include Enumerable
***************
*** 189,199 ****
          end
        end
- 
-       # Go through all Mapping objects linked to this marker.
-       def each
-         self.mappings_as_marker.each do |mapping|
-           yield mapping
-         end
-       end
        
        # Check whether this marker is mapped to a given Bio::Map::SimpleMap.
--- 203,206 ----
***************
*** 238,241 ****
--- 245,249 ----
        end
        
+ 
      end #ActsLikeMarker
  	  
***************
*** 253,257 ****
        # * _marker_: a Bio::Map::Marker object
        # * _location_: a Bio::Locations object
- 
        def initialize (map, marker, location = nil)
          @map, @marker, @location = map, marker, location
--- 261,264 ----
***************
*** 259,280 ****
        attr_accessor :map, :marker, :location
        
! #       # Compares the location of this mapping to another mapping.
! #       # ---
! #       # *Arguments*:
! #       # * other_mapping: Bio::Map::Mapping object
! #       # *Returns*::
! #       # * 1 if self < other location
! #       # * -1 if self > other location
! #       # * 0 if both location are the same
! #       # * nil if the argument is not a Bio::Location object
! #       def <=>(other)
! #         unless other.kind_of?(Bio::Map::Mapping)
! #           raise "[Error] markers are not comparable"
! #         end
! #         unless @map.equal?(other.map)
! #           raise "[Error] maps have to be the same"
! #         end
! #         return self.location<=>(other.location) # FIXME: no <=>-method in Bio::Locations
! #       end
      end # Mapping
      
--- 266,288 ----
        attr_accessor :map, :marker, :location
        
!       # Compares the location of this mapping to another mapping.
!       # ---
!       # *Arguments*:
!       # * other_mapping: Bio::Map::Mapping object
!       # *Returns*::
!       # * 1 if self < other location
!       # * -1 if self > other location
!       # * 0 if both location are the same
!       # * nil if the argument is not a Bio::Location object
!       def <=>(other)
!         unless other.kind_of?(Bio::Map::Mapping)
!           raise "[Error] markers are not comparable"
!         end
! 	    unless @map.equal?(other.map)
!           raise "[Error] maps have to be the same"
!         end
! 
!         return self.location.<=>(other.location)
!       end
      end # Mapping
      



From aerts at dev.open-bio.org  Tue Jun 27 12:40:17 2006
From: aerts at dev.open-bio.org (Jan Aerts)
Date: Tue, 27 Jun 2006 12:40:17 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio map.rb,1.7,1.8
Message-ID: <200606271240.k5RCeHJA008800@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv8780/lib/bio

Modified Files:
	map.rb 
Log Message:
Forgot to remove reference to Enumerable.


Index: map.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/map.rb,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** map.rb	27 Jun 2006 12:37:42 -0000	1.7
--- map.rb	27 Jun 2006 12:40:15 -0000	1.8
***************
*** 6,10 ****
  # Licence::     Ruby's
  #
! # $Id:
  require 'bio/location'
  
--- 6,10 ----
  # Licence::     Ruby's
  #
! # $Id$
  require 'bio/location'
  
***************
*** 92,97 ****
    #    end
      module ActsLikeMap
-       include Enumerable
-       
        # = DESCRIPTION
        # Adds a Bio::Map::Mappings object to its array of mappings.
--- 92,95 ----
***************
*** 169,174 ****
      #    end
      module ActsLikeMarker
-       include Enumerable
-       
        # = DESCRIPTION
        # Adds a Bio::Map::Mappings object to its array of mappings.
--- 167,170 ----



From ngoto at dev.open-bio.org  Tue Jun 27 14:23:47 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Tue, 27 Jun 2006 14:23:47 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/db/pdb pdb.rb,1.15,1.16
Message-ID: <200606271423.k5RENlQb009267@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/db/pdb
In directory dev.open-bio.org:/tmp/cvs-serv9227/lib/bio/db/pdb

Modified Files:
	pdb.rb 
Log Message:
Bio::PDB::ATOM#name, #resName, #iCode, #chaarge are changed to be strippedi
when initializing.
Bio::PDB::ATOM#segID is changed to be right-stripped when initializing.
Bio::PDB::ATOM#element is changed to be left-stripped when initializing.
(Because Bio::PDB::HETATM inherits Bio::PDB::ATOM, Bio::PDB::HETATM is
also subject to the changes.)


Index: pdb.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb/pdb.rb,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** pdb.rb	20 Feb 2006 13:00:43 -0000	1.15
--- pdb.rb	27 Jun 2006 14:23:45 -0000	1.16
***************
*** 993,1002 ****
            return self if @parsed
            self.serial     = @str[6..10].to_i
!           self.name       = @str[12..15]
            self.altLoc     = @str[16..16]
!           self.resName    = @str[17..19].rstrip
            self.chainID    = @str[21..21]
            self.resSeq     = @str[22..25].to_i
!           self.iCode      = @str[26..26]
            self.x          = @str[30..37].to_f
            self.y          = @str[38..45].to_f
--- 993,1002 ----
            return self if @parsed
            self.serial     = @str[6..10].to_i
!           self.name       = @str[12..15].strip
            self.altLoc     = @str[16..16]
!           self.resName    = @str[17..19].strip
            self.chainID    = @str[21..21]
            self.resSeq     = @str[22..25].to_i
!           self.iCode      = @str[26..26].strip
            self.x          = @str[30..37].to_f
            self.y          = @str[38..45].to_f
***************
*** 1004,1010 ****
            self.occupancy  = @str[54..59].to_f
            self.tempFactor = @str[60..65].to_f
!           self.segID      = @str[72..75]
!           self.element    = @str[76..77]
!           self.charge     = @str[78..79]
            @parsed = true
            self
--- 1004,1010 ----
            self.occupancy  = @str[54..59].to_f
            self.tempFactor = @str[60..65].to_f
!           self.segID      = @str[72..75].to_s.rstrip
!           self.element    = @str[76..77].to_s.lstrip
!           self.charge     = @str[78..79].to_s.strip
            @parsed = true
            self
***************
*** 1012,1019 ****
  
          def to_s
            sprintf("%-6s%5d %-4s%-1s%3s %-1s%4d%-1s   %8.3f%8.3f%8.3f%6.2f%6.2f      %-4s%2s%-2s\n",
                    self.record_name,
                    self.serial, 
!                   self.name,
                    self.altLoc,
                    self.resName,
--- 1012,1024 ----
  
          def to_s
+           atomname = self.name.to_s
+           elem = self.element.to_s.strip
+           if elem.length == 1 and atomname.lstrip[0, 1] == elem then
+             atomname = ' ' + atomname
+           end
            sprintf("%-6s%5d %-4s%-1s%3s %-1s%4d%-1s   %8.3f%8.3f%8.3f%6.2f%6.2f      %-4s%2s%-2s\n",
                    self.record_name,
                    self.serial, 
!                   atomname,
                    self.altLoc,
                    self.resName,



From ngoto at dev.open-bio.org  Tue Jun 27 14:25:42 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Tue, 27 Jun 2006 14:25:42 +0000
Subject: [BioRuby-cvs] bioruby/test/unit/bio/db/pdb test_pdb.rb,1.1,1.2
Message-ID: <200606271425.k5REPgfp009296@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/test/unit/bio/db/pdb
In directory dev.open-bio.org:/tmp/cvs-serv9276/test/unit/bio/db/pdb

Modified Files:
	test_pdb.rb 
Log Message:
* License is changed to Ruby's.
* Follow changes to pdb.rb (as is nearly the same behavior as bioruby-0.6.4).


Index: test_pdb.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/db/pdb/test_pdb.rb,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** test_pdb.rb	26 Jan 2006 16:06:03 -0000	1.1
--- test_pdb.rb	27 Jun 2006 14:25:40 -0000	1.2
***************
*** 5,29 ****
  #             Naohisa Goto <ng at bioruby.org>
  #
! # License:: LGPL
  #
  #  $Id$
  #
- #--
- #  This library is free software; you can redistribute it and/or
- #  modify it under the terms of the GNU Lesser General Public
- #  License as published by the Free Software Foundation; either
- #  version 2 of the License, or (at your option) any later version.
- #
- #  This library is distributed in the hope that it will be useful,
- #  but WITHOUT ANY WARRANTY; without even the implied warranty of
- #  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- #  Lesser General Public License for more details.
- #
- #  You should have received a copy of the GNU Lesser General Public
- #  License along with this library; if not, write to the Free Software
- #  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
- #++
- #
- #
  
  require 'pathname'
--- 5,12 ----
  #             Naohisa Goto <ng at bioruby.org>
  #
! # License:: Ruby's
  #
  #  $Id$
  #
  
  require 'pathname'
***************
*** 58,62 ****
  
        def test_name
!         assert_equal(' CG2', @atom.name)
        end
  
--- 41,45 ----
  
        def test_name
!         assert_equal('CG2', @atom.name)
        end
  
***************
*** 78,82 ****
  
        def test_iCode
!         assert_equal(' ', @atom.iCode)
        end
  
--- 61,65 ----
  
        def test_iCode
!         assert_equal('', @atom.iCode)
        end
  
***************
*** 102,114 ****
  
        def test_segID
!         assert_equal('A1  ', @atom.segID)
        end
  
        def test_element
!         assert_equal(' C', @atom.element)
        end
  
        def test_charge
!         assert_equal('  ', @atom.charge)
        end
  
--- 85,97 ----
  
        def test_segID
!         assert_equal('A1', @atom.segID)
        end
  
        def test_element
!         assert_equal('C', @atom.element)
        end
  
        def test_charge
!         assert_equal('', @atom.charge)
        end
  



From ngoto at dev.open-bio.org  Tue Jun 27 15:17:09 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Tue, 27 Jun 2006 15:17:09 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/blat report.rb,1.9,1.10
Message-ID: <200606271517.k5RFH9w8009506@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl/blat
In directory dev.open-bio.org:/tmp/cvs-serv9484/lib/bio/appl/blat

Modified Files:
	report.rb 
Log Message:
changed documents


Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blat/report.rb,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** report.rb	20 Jun 2006 14:34:38 -0000	1.9
--- report.rb	27 Jun 2006 15:17:07 -0000	1.10
***************
*** 34,38 ****
      # On the other hand, in many other homology search programs,
      # the start position of a sequence is numbered as 1.
!     # To keep compatibility, the BLAT parser adds 1 to every position number.
      #
      # Note that Bio::Blat::Report#query_def, #query_id, #query_len  methods
--- 34,39 ----
      # On the other hand, in many other homology search programs,
      # the start position of a sequence is numbered as 1.
!     # To keep compatibility, the BLAT parser adds 1 to every position number
!     # except Bio::Blat::Report::Seqdesc and some Bio::Blat specific methods.
      #
      # Note that Bio::Blat::Report#query_def, #query_id, #query_len  methods
***************
*** 335,346 ****
          #--
          # methods described in the BLAT FAQ at the UCSC genome browser.
!         # (http://genome.ucsc.edu/FAQ/FAQblat#blat5)
          #++
  
          # Calculates the pslCalcMilliBad value defined in the
!         # BLAT FAQ (http://genome.ucsc.edu/FAQ/FAQblat#blat5).
          #
          # The algorithm is taken from the BLAT FAQ
!         # (http://genome.ucsc.edu/FAQ/FAQblat#blat5).
          def milli_bad
            w = (self.protein? ? 3 : 1)
--- 336,347 ----
          #--
          # methods described in the BLAT FAQ at the UCSC genome browser.
!         # (http://genome.ucsc.edu/FAQ/FAQblat#blat4)
          #++
  
          # Calculates the pslCalcMilliBad value defined in the
!         # BLAT FAQ (http://genome.ucsc.edu/FAQ/FAQblat#blat4).
          #
          # The algorithm is taken from the BLAT FAQ
!         # (http://genome.ucsc.edu/FAQ/FAQblat#blat4).
          def milli_bad
            w = (self.protein? ? 3 : 1)
***************
*** 359,366 ****
          # Calculates the percent identity compatible with the BLAT web server
          # as described in the BLAT FAQ
!         # (http://genome.ucsc.edu/FAQ/FAQblat#blat5).
          #
          # The algorithm is taken from the BLAT FAQ
!         # (http://genome.ucsc.edu/FAQ/FAQblat#blat5).
          def percent_identity
            100.0 - self.milli_bad * 0.1
--- 360,367 ----
          # Calculates the percent identity compatible with the BLAT web server
          # as described in the BLAT FAQ
!         # (http://genome.ucsc.edu/FAQ/FAQblat#blat4).
          #
          # The algorithm is taken from the BLAT FAQ
!         # (http://genome.ucsc.edu/FAQ/FAQblat#blat4).
          def percent_identity
            100.0 - self.milli_bad * 0.1
***************
*** 372,376 ****
          #
          # The algorithm is taken from the BLAT FAQ
!         # (http://genome.ucsc.edu/FAQ/FAQblat#blat5).
          def protein?
            return nil if self.block_sizes.empty?
--- 373,377 ----
          #
          # The algorithm is taken from the BLAT FAQ
!         # (http://genome.ucsc.edu/FAQ/FAQblat#blat4).
          def protein?
            return nil if self.block_sizes.empty?
***************
*** 397,404 ****
          # Calculates the score compatible with the BLAT web server
          # as described in the BLAT FAQ
!         # (http://genome.ucsc.edu/FAQ/FAQblat#blat5).
          #
          # The algorithm is taken from the BLAT FAQ
!         # (http://genome.ucsc.edu/FAQ/FAQblat#blat5).
          def score
            w = (self.protein? ? 3 : 1)
--- 398,405 ----
          # Calculates the score compatible with the BLAT web server
          # as described in the BLAT FAQ
!         # (http://genome.ucsc.edu/FAQ/FAQblat#blat4).
          #
          # The algorithm is taken from the BLAT FAQ
!         # (http://genome.ucsc.edu/FAQ/FAQblat#blat4).
          def score
            w = (self.protein? ? 3 : 1)



From ngoto at dev.open-bio.org  Wed Jun 28 13:43:33 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Wed, 28 Jun 2006 13:43:33 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/blat report.rb,1.10,1.11
Message-ID: <200606281343.k5SDhXq7013712@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl/blat
In directory dev.open-bio.org:/tmp/cvs-serv13692/lib/bio/appl/blat

Modified Files:
	report.rb 
Log Message:
* Fixed a bug in Bio::Blat::Report::Hit#protein?.
* Fixed: when protein query and nucleotide database, HSPs are incorrect.


Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blat/report.rb,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** report.rb	27 Jun 2006 15:17:07 -0000	1.10
--- report.rb	28 Jun 2006 13:43:31 -0000	1.11
***************
*** 140,149 ****
          # It is designed to be called internally from Bio::Blat::Report class.
          # Users shall not use it directly.
!         def initialize(query_len, strand,
!                        blksize, qstart, tstart, qseq, tseq)
            @blocksize  = blksize
            @qseq       = qseq
            @hseq       = hseq
            @hit_strand   = 'plus'
            case strand
            when '-'
--- 140,151 ----
          # It is designed to be called internally from Bio::Blat::Report class.
          # Users shall not use it directly.
!         def initialize(query_len, target_len, strand,
!                        blksize, qstart, tstart, qseq, tseq,
!                        protein_flag)
            @blocksize  = blksize
            @qseq       = qseq
            @hseq       = hseq
            @hit_strand   = 'plus'
+           w = (protein_flag ? 3 : 1) # 3 means query=protein target=dna
            case strand
            when '-'
***************
*** 156,161 ****
              # we add 1 to each position number.
              @hit_from   = tstart + 1
!             @hit_to     = tstart + blksize # - 1 + 1
!           else #when '+'
              @query_strand = 'plus'
              # To keep compatibility with other homology search programs,
--- 158,174 ----
              # we add 1 to each position number.
              @hit_from   = tstart + 1
!             @hit_to     = tstart + blksize * w # - 1 + 1
!           when '+-'
!             # hit is minus strand
!             @query_strand = 'plus'
!             @hit_strand = 'minus'
!             # To keep compatibility, with other homology search programs,
!             # we add 1 to each position number.
!             @query_from   = qstart + 1
!             @query_to     = qstart + blksize # - 1 + 1
!             # convert positions
!             @hit_from     = target_len - tstart
!             @hit_to       = target_len - tstart - blksize * w + 1
!           else #when '+', '++'
              @query_strand = 'plus'
              # To keep compatibility with other homology search programs,
***************
*** 164,168 ****
              @query_to   = qstart + blksize # - 1 + 1
              @hit_from   = tstart + 1
!             @hit_to     = tstart + blksize # - 1 + 1
            end
          end
--- 177,181 ----
              @query_to   = qstart + blksize # - 1 + 1
              @hit_from   = tstart + 1
!             @hit_to     = tstart + blksize * w # - 1 + 1
            end
          end
***************
*** 298,304 ****
              qseqs = query.seqs
              tseqs = target.seqs
              @blocks = (0...block_count).collect do |i|
!               SegmentPair.new(query.size, strand, bs[i],
!                               qst[i], tst[i], qseqs[i], tseqs[i])
              end
            end
--- 311,319 ----
              qseqs = query.seqs
              tseqs = target.seqs
+             pflag = self.protein?
              @blocks = (0...block_count).collect do |i|
!               SegmentPair.new(query.size, target.size, strand, bs[i],
!                               qst[i], tst[i], qseqs[i], tseqs[i],
!                               pflag)
              end
            end
***************
*** 374,380 ****
          # The algorithm is taken from the BLAT FAQ
          # (http://genome.ucsc.edu/FAQ/FAQblat#blat4).
          def protein?
            return nil if self.block_sizes.empty?
!           case self.strand
            when '+'
              if self.target.end == self.target.starts[-1] +
--- 389,398 ----
          # The algorithm is taken from the BLAT FAQ
          # (http://genome.ucsc.edu/FAQ/FAQblat#blat4).
+         #
+         # Note: It seems that it returns true only when protein query
+         # with nucleotide database (blat options: -q=prot -t=dnax).
          def protein?
            return nil if self.block_sizes.empty?
!           case self.strand[1,1]
            when '+'
              if self.target.end == self.target.starts[-1] +
***************
*** 386,390 ****
            when '-'
              if self.target.start == self.target.size -
!                 self.target.starts[-1] + 3 * self.block_sizes[-1] then
                true
              else
--- 404,408 ----
            when '-'
              if self.target.start == self.target.size -
!                 self.target.starts[-1] - 3 * self.block_sizes[-1] then
                true
              else



From ngoto at dev.open-bio.org  Thu Jun 29 11:54:35 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Thu, 29 Jun 2006 11:54:35 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/blat report.rb,1.11,1.12
Message-ID: <200606291154.k5TBsZud023085@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl/blat
In directory dev.open-bio.org:/tmp/cvs-serv23065/lib/bio/appl/blat

Modified Files:
	report.rb 
Log Message:
* psl without header is supported.
* New attribute ``psl_version'' is added.


Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blat/report.rb,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** report.rb	28 Jun 2006 13:43:31 -0000	1.11
--- report.rb	29 Jun 2006 11:54:33 -0000	1.12
***************
*** 59,62 ****
--- 59,67 ----
              @hits << Hit.new(line)
            else
+             # for headerless data
+             if /^\d/ =~ line then
+               flag = true
+               redo
+             end
              line = line.chomp
              if /\A\-+\s*\z/ =~ line
***************
*** 81,85 ****
        # Parses headers.
        def parse_header(ary)
!         ary.shift # first line is removed
          a0 = ary.collect { |x| x.split(/\t/) }
          k = []
--- 86,98 ----
        # Parses headers.
        def parse_header(ary)
!         while x = ary.shift
!           if /psLayout version (\S+)/ =~ x then
!             @psl_version = $1
!             break
!           elsif !(x.strip.empty?)
!             ary.unshift(x)
!             break
!           end
!         end
          a0 = ary.collect { |x| x.split(/\t/) }
          k = []
***************
*** 95,98 ****
--- 108,114 ----
        private :parse_header
  
+       # version of the psl format (String or nil).
+       attr_reader :psl_version
+ 
        # Bio::Blat::Report::SeqDesc stores sequence information of
        # query or subject of the BLAT report.